perses.storage.NetCDFStorage

class perses.storage.NetCDFStorage(filename, mode='w')

NetCDF storage layer.

Methods

close()	Close the storage layer.
get_object(envname, modname, varname[, …])	Get the serialized Python object.
sync()	Flush write buffer.
write_array(varname, array[, iteration])	Write a numpy array as a native NetCDF array
write_configuration(varname, positions, topology)	Write a configuration (or one of a sequence of configurations) to be stored as a native NetCDF array
write_object(varname, obj[, iteration])	Serialize a Python object, encoding as pickle when storing as string in NetCDF.
write_quantity(varname, value[, iteration])	Write a floating-point number

__init__(filename, mode='w')

Create NetCDF storage layer, creating or appending to an existing file.

Parameters:

filename : str

Name of storage file to bind to.

mode : str, optional, default=’w’

File open mode, ‘w’ for (over)write, ‘a’ for append.

Methods

__init__(filename[, mode])	Create NetCDF storage layer, creating or appending to an existing file.
close()	Close the storage layer.
get_object(envname, modname, varname[, …])	Get the serialized Python object.
sync()	Flush write buffer.
write_array(varname, array[, iteration])	Write a numpy array as a native NetCDF array
write_configuration(varname, positions, topology)	Write a configuration (or one of a sequence of configurations) to be stored as a native NetCDF array
write_object(varname, obj[, iteration])	Serialize a Python object, encoding as pickle when storing as string in NetCDF.
write_quantity(varname, value[, iteration])	Write a floating-point number

close()

Close the storage layer.

get_object(envname, modname, varname, iteration=None)

Get the serialized Python object.

Parameters:

envname : str

The name of the environment for the variable

modname : str

The name of the module for the variable

varname : str

The variable name to be stored

iteration : int, optional, default=None

The local iteration for the module, or None if this is a singleton

Returns:

obj : object

The retrieved object

sync()

Flush write buffer.

write_array(varname, array, iteration=None)

Write a numpy array as a native NetCDF array

Parameters:

varname : str

The variable name to be stored

array : numpy.array of arbitrary dimension

The numpy array to be written

iteration : int, optional, default=None

The local iteration for the module, or None if this is a singleton

write_configuration(varname, positions, topology, iteration=None, frame=None, nframes=None)

Write a configuration (or one of a sequence of configurations) to be stored as a native NetCDF array

Parameters:

varname : str

The variable name to be stored

positions : simtk.unit.Quantity of size [natoms,3] with units compatible with angstroms

The positions to be written

topology : md.Topology object

The corresponding Topology object

iteration : int, optional, default=None

The local iteration for the module, or None if this is a singleton

frame : int, optional, default=None

If these coordinates are part of multiple frames in a sequence, the frame number

nframes : int, optional, default=None

If these coordinates are part of multiple frames in a sequence, the total number of frames in the sequence

write_object(varname, obj, iteration=None)

Serialize a Python object, encoding as pickle when storing as string in NetCDF.

Parameters:

varname : str

The variable name to be stored

obj : object

The object to be serialized

iteration : int, optional, default=None

The local iteration for the module, or None if this is a singleton

write_quantity(varname, value, iteration=None)

Write a floating-point number

Parameters:

varname : str

The variable name to be stored

value : float

The floating-point value to be written

iteration : int, optional, default=None

The local iteration for the module, or None if this is a singleton