def open_old(cls, fname):
"""
Opens the NetCDF file and sets the global attributes that the file sets
"""
inst = cls(fname, 'r')
ncfile = inst._ncfile
inst.Conventions = ncfile.Conventions
inst.ConventionVersion = ncfile.ConventionVersion
inst.application = ncfile.application
inst.program = ncfile.program
inst.programVersion = ncfile.programVersion
inst.title = ncfile.title
# Set up the dimensions as attributes
for dim in ncfile.dimensions:
# Exception for ParmEd-created ncrst files
if dim == 'time': continue
setattr(inst, dim, amber.get_int_dimension(ncfile, dim))
inst.hasvels = 'velocities' in ncfile.variables
inst.hasbox = ('cell_lengths' in ncfile.variables and
'cell_angles' in ncfile.variables)
if inst.hasvels:
vels = ncfile.variables['velocities']
inst.velocity_scale = vels.scale_factor
# Turn off automatic scaling for netCDF4. Ugh.
try:
vels.set_auto_maskandscale(False)
except AttributeError:
# Other packages do not have this variable
pass
return inst
def open_old(cls, fname):
"""
Opens the NetCDF file and sets the global attributes that the file sets
Parameters:
- fname (string): File name of the trajectory to open. It must
exist
"""
inst = cls(fname, 'r')
ncfile = inst._ncfile
inst.Conventions = ncfile.Conventions
inst.ConventionVersion = ncfile.ConventionVersion
inst.application = ncfile.application
inst.program = ncfile.program
inst.programVersion = ncfile.programVersion
inst.title = ncfile.title
# Set up the dimensions as attributes
for dim in ncfile.dimensions:
setattr(inst, dim, amber.get_int_dimension(ncfile, dim))
inst.hascrds = 'coordinates' in ncfile.variables
inst.hasvels = 'velocities' in ncfile.variables
inst.hasfrcs = 'forces' in ncfile.variables
inst.hasbox = ('cell_lengths' in ncfile.variables and
'cell_angles' in ncfile.variables)
if inst.hasvels:
inst.velocity_scale = ncfile.variables['velocities'].scale_factor
if inst.frame is None:
if 'time' in ncfile.variables:
inst.frame = len(ncfile.variables['time'][:])
elif inst.hascrds:
inst.frame = len(ncfile.variables['coordinates'][:])
elif inst.hasvels:
inst.frame = len(ncfile.variables['velocities'][:])
elif inst.hasfrcs:
inst.frame = len(ncfile.variables['forces'][:])
return inst
