def test_unit_0():
a = np.array([1.0])
b = in_units_of(a, 'nanometers', 'angstroms', inplace=False)
c = in_units_of(a, 'angstroms', 'nanometers', inplace=False)
eq(b, np.array([10.0]))
eq(c, np.array([0.1]))
assert a.ctypes.data != b.ctypes.data
assert a.ctypes.data != c.ctypes.data
def test_unit_0():
a = np.array([1.0])
b = in_units_of(a, 'nanometers', 'angstroms', inplace=False)
c = in_units_of(a, 'angstroms', 'nanometers', inplace=False)
eq(b, np.array([10.0]))
eq(c, np.array([0.1]))
assert a.ctypes.data != b.ctypes.data
assert a.ctypes.data != c.ctypes.data
def test_unit_1():
a = np.array([1.0])
b = in_units_of(a, 'nanometers', 'angstroms', inplace=True)
eq(a, np.array([10.0]))
eq(b, np.array([10.0]))
# a and b point to the same memory
assert a.ctypes.data == b.ctypes.data
def test_unit_1():
a = np.array([1.0])
b = in_units_of(a, 'nanometers', 'angstroms', inplace=True)
eq(a, np.array([10.0]))
eq(b, np.array([10.0]))
# a and b point to the same memory
assert a.ctypes.data == b.ctypes.data
def test_unit_2():
a = np.array([1.0])
a.flags['WRITEABLE'] = False
b = in_units_of(a, 'nanometers', 'angstroms', inplace=True)
eq(b, np.array([10.0]))
# a and b do not point to the same memory, since a isn't writeable
assert a.ctypes.data != b.ctypes.data
def test_unit_2():
a = np.array([1.0])
a.flags['WRITEABLE'] = False
b = in_units_of(a, 'nanometers', 'angstroms', inplace=True)
eq(b, np.array([10.0]))
# a and b do not point to the same memory, since a isn't writeable
assert a.ctypes.data != b.ctypes.data
def test_unit_3():
eq(1000000.0, in_units_of(1, 'meter**2/second',
'nanometers**2/picosecond'))
def test_unit_3():
eq(1000000.0, in_units_of(1, 'meter**2/second', 'nanometers**2/picosecond'))
def iterload(filename, chunk=100, **kwargs):
"""An iterator over a trajectory from one or more files on disk, in fragments
This may be more memory efficient than loading an entire trajectory at
once
Parameters
----------
filename : str
Path to the trajectory file on disk
chunk : int
Number of frames to load at once from disk per iteration. If 0, load all.
Other Parameters
----------------
top : {str, Trajectory, Topology}
Most trajectory formats do not contain topology information. Pass in
either the path to a RCSB PDB file, a trajectory, or a topology to
supply this information. This option is not required for the .h5, .lh5,
and .pdb formats, which already contain topology information.
stride : int, default=None
Only read every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the
file. This may be slightly slower than the standard read because it
requires an extra copy, but will save memory.
See Also
--------
load, load_frame
Examples
--------
>>> import mdtraj as md
>>> for chunk in md.iterload('output.xtc', top='topology.pdb')
>>> print chunk
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
"""
stride = kwargs.get('stride', 1)
atom_indices = cast_indices(kwargs.get('atom_indices', None))
if chunk % stride != 0 and filename.endswith('.dcd'):
raise ValueError('Stride must be a divisor of chunk. stride=%d does not go '
'evenly into chunk=%d' % (stride, chunk))
if chunk == 0:
yield load(filename, **kwargs)
# If chunk was 0 then we want to avoid filetype-specific code in case of undefined behavior in various file parsers.
else:
skip = kwargs.get('skip', 0)
if filename.endswith('.h5'):
if 'top' in kwargs:
warnings.warn('top= kwarg ignored since file contains topology information')
with HDF5TrajectoryFile(filename) as f:
if skip > 0:
xyz, _, _, _ = f.read(skip, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
if atom_indices is None:
topology = f.topology
else:
topology = f.topology.subset(atom_indices)
while True:
data = f.read(chunk*stride, stride=stride, atom_indices=atom_indices)
if data == []:
raise StopIteration()
in_units_of(data.coordinates, f.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(data.cell_lengths, f.distance_unit, Trajectory._distance_unit, inplace=True)
yield Trajectory(xyz=data.coordinates, topology=topology,
time=data.time, unitcell_lengths=data.cell_lengths,
unitcell_angles=data.cell_angles)
if filename.endswith('.lh5'):
if 'top' in kwargs:
warnings.warn('top= kwarg ignored since file contains topology information')
with LH5TrajectoryFile(filename) as f:
if atom_indices is None:
topology = f.topology
else:
topology = f.topology.subset(atom_indices)
ptr = 0
if skip > 0:
xyz, _, _, _ = f.read(skip, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
while True:
xyz = f.read(chunk*stride, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
time = np.arange(ptr, ptr+len(xyz)*stride, stride)
ptr += len(xyz)*stride
yield Trajectory(xyz=xyz, topology=topology, time=time)
elif filename.endswith('.xtc'):
topology = _parse_topology(kwargs.get('top', None))
with XTCTrajectoryFile(filename) as f:
if skip > 0:
xyz, _, _, _ = f.read(skip)
if len(xyz) == 0:
raise StopIteration()
while True:
xyz, time, step, box = f.read(chunk*stride, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(box, f.distance_unit, Trajectory._distance_unit, inplace=True)
trajectory = Trajectory(xyz=xyz, topology=topology, time=time)
trajectory.unitcell_vectors = box
yield trajectory
elif filename.endswith('.dcd'):
topology = _parse_topology(kwargs.get('top', None))
with DCDTrajectoryFile(filename) as f:
ptr = 0
if skip > 0:
xyz, _, _ = f.read(skip, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
while True:
# for reasons that I have not investigated, dcdtrajectory file chunk and stride
# together work like this method, but HDF5/XTC do not.
xyz, box_length, box_angle = f.read(chunk, stride=stride, atom_indices=atom_indices)
if len(xyz) == 0:
raise StopIteration()
in_units_of(xyz, f.distance_unit, Trajectory._distance_unit, inplace=True)
in_units_of(box_length, f.distance_unit, Trajectory._distance_unit, inplace=True)
time = np.arange(ptr, ptr+len(xyz)*stride, stride)
ptr += len(xyz)*stride
yield Trajectory(xyz=xyz, topology=topology, time=time, unitcell_lengths=box_length,
unitcell_angles=box_angle)
else:
log.critical("loading complete traj into mem! This might no be desired.")
t = load(filename, **kwargs)
for i in range(skip, len(t), chunk):
yield t[i:i+chunk]
def test_unit_2_bytes():
a = in_units_of(1, b'meter**2/second', b'nanometers**2/picosecond')
b = 1e-6
assert abs(a-b) < 1e-10
def test_unit_1():
assert 1 == in_units_of(100, 'meter', 'centimeter')