def id_format(filename):
""" Identifies the file type as an Amber NetCDF trajectory file
Parameters
----------
filename : str
Name of the file to check format for
Returns
-------
is_fmt : bool
True if it is an Amber NetCDF trajectory file. False otherwise
Notes
-----
Remote NetCDF files cannot be loaded
"""
if filename.startswith('http://') or filename.startswith('https://')\
or filename.startswith('ftp://'):
return False
try:
f = NetCDFFile(filename, 'r', mmap=False)
except (TypeError, OSError):
return False
try:
try:
if f.Conventions.decode() != 'AMBER':
return False
except AttributeError:
return False
# Passed all our tests
return True
finally:
f.close()
def __init__(self, fname, mode='r'):
"""
Opens a NetCDF File. The main constructor should never be called
directly. The alternative "open_old" and "open_new" constructors should
be called instead for reading existing or writing new NetCDF files,
respectively.
"""
self.closed = False
self._ncfile = NetCDFFile(fname, mode, mmap=False)
def __init__(self, fname, mode='r'):
""" Opens a NetCDF File """
self.closed = False
if mode.startswith('w') and nc is not None:
self._ncfile = nc.Dataset(fname, mode, format='NETCDF3_64BIT')
else:
if mode.startswith('w'):
warnings.warn('Could not find netCDF4 module. Falling back on '
'scipy implementation, which can significantly '
'slow down simulations if used as a reporter')
self._ncfile = NetCDFFile(fname, mode, mmap=False)
def __init__(self, fname, mode='r'):
"""
Opens a NetCDF File. The main constructor should never be called
directly. The alternative "open_old" and "open_new" constructors should
be called instead for reading existing or writing new NetCDF files,
respectively.
"""
self.closed = False
if mode.startswith('w') and nc is not None:
self._ncfile = nc.Dataset(fname, mode, format='NETCDF3_64BIT')
else:
if mode.startswith('w'):
warnings.warn('Could not find netCDF4 module. Falling back on '
'scipy implementation, which can significantly '
'slow down simulations if used as a reporter')
self._ncfile = NetCDFFile(fname, mode, mmap=False)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom,
box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom,
rst.hasbox,
rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f',
('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True),
'w',
mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial', ))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)
def testNetCDF(self):
""" Test scipy NetCDF parsing """
traj = NetCDFTraj.open_old(get_fn('tz2.truncoct.nc'))
self._check_traj(traj)
rst = NetCDFRestart.open_old(get_fn('ncinpcrd.rst7'))
self._check_rst(rst)
# Now try writing files
ntraj = NetCDFTraj.open_new(get_fn('test.nc', written=True),
traj.atom, box=True)
for crd in traj.coordinates:
ntraj.add_coordinates(crd)
for box in traj.box:
ntraj.add_box(box)
ntraj.close()
traj = NetCDFTraj.open_old(get_fn('test.nc', written=True))
self._check_traj(traj, written=True)
nrst = NetCDFRestart.open_new(get_fn('test.ncrst', written=True),
rst.atom, rst.hasbox, rst.hasvels,
title=rst.title)
nrst.coordinates = rst.coordinates
nrst.velocities = rst.velocities
nrst.time = rst.time
nrst.box = rst.box
nrst.close()
rst = NetCDFRestart.open_old(get_fn('test.ncrst', written=True))
self._check_rst(rst, written=True)
# Now write NetCDF trajectory without any optional attributes/variables
# and check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(nframe, natom, 3) * 20 - 10
coords = np.array(coords, dtype='f')
nctraj = NetCDFFile(get_fn('test2.nc', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBER'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'f', ('frame', 'atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFTraj.open_old(get_fn('test2.nc', written=True))
np.testing.assert_allclose(traj2.coordinates, coords)
# Now write NetCDF restart without any optional attributes/variables and
# check proper reading
natom = randint(100, 1000)
nframe = randint(5, 20)
coords = np.random.rand(natom, 3) * 20 - 10
nctraj = NetCDFFile(get_fn('test2.ncrst', written=True), 'w', mmap=False)
nctraj.Conventions = 'AMBERRESTART'
nctraj.ConventionVersion = '1.0'
nctraj.program = 'ParmEd'
nctraj.programVersion = __version__
nctraj.createDimension('frame', None)
nctraj.createDimension('spatial', 3)
nctraj.createDimension('atom', natom)
v = nctraj.createVariable('spatial', 'c', ('spatial',))
v[:] = np.asarray(list('xyz'))
v = nctraj.createVariable('coordinates', 'd', ('atom', 'spatial'))
v[:] = coords
del v
nctraj.close()
traj2 = NetCDFRestart.open_old(get_fn('test2.ncrst', written=True))
np.testing.assert_allclose(traj2.coordinates[0], coords)
def __init__(self, fname, mode='r'):
""" Opens a NetCDF File """
self.closed = False
self._ncfile = NetCDFFile(fname, mode, mmap=False)