biotite.structure.io.npz.NpzFile¶

class biotite.structure.io.npz.NpzFile[source]¶

Bases: File

This class represents a NPZ file, the preferable format for Biotite internal structure storage.

Internally the this class writes/reads all attribute arrays of an AtomArray or AtomArrayStack using the NumPy save()/load() method. This format offers the fastest I/O operations and completely preserves the content all atom annotation arrays.

Examples

Load a \*.npz file, modify the structure and save the new structure into a new file:

>>> import os.path
>>> file = NpzFile.read(os.path.join(path_to_structures, "1l2y.npz"))
>>> array_stack = file.get_structure()
>>> array_stack_mod = rotate(array_stack, [1,2,3])
>>> file = NpzFile()
>>> file.set_structure(array_stack_mod)
>>> file.write(os.path.join(path_to_directory, "1l2y_mod.npz"))

copy()¶

Create a deep copy of this object.

Returns:

copy: A copy of this object.

get_structure()¶

Get an AtomArray or AtomArrayStack from the file.

If this method returns an array or stack depends on which type of object was used when the file was written.

Returns:

arrayAtomArray or AtomArrayStack: The array or stack contained in this file.

classmethod read(file)¶

Read a NPZ file.

Parameters:

filefile-like object or str: The file to be read. Alternatively a file path can be supplied.

Returns:

file_objectNPZFile: The parsed file.

set_structure(array)¶

Set the AtomArray or AtomArrayStack for the file.

Parameters:

arrayAtomArray or AtomArrayStack: The array or stack to be saved into this file.

write(file)¶

Write a NPZ file.

Parameters:

filefile-like object or str: The file to be read. Alternatively, a file path can be supplied.