biotite.structure.io.mmtf.MMTFFile¶

class biotite.structure.io.mmtf.MMTFFile[source]¶

Bases: File, MutableMapping

This class represents a MMTF file.

When reading a file, the MessagePack unpacker is used to create a dictionary of the file content. This dictionary is accessed by indexing the MMTFFile instance directly with the dictionary keys. If the dictionary value is an encoded array, the value automatically decoded. Decoded arrays are always returned as ndarray instances.

Examples

>>> import os.path
>>> mmtf_file = MMTFFile.read(os.path.join(path_to_structures, "1l2y.mmtf"))
>>> print(mmtf_file["title"])
NMR Structure of Trp-Cage Miniprotein Construct TC5b
>>> print(mmtf_file["chainNameList"])
['A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A'
 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A' 'A'
 'A' 'A']

clear() → None. Remove all items from D.¶

copy()¶

Create a deep copy of this object.

Returns:

copy: A copy of this object.

get(k[, d]) → D[k] if k in D, else d. d defaults to None.¶

get_codec(key)¶

Obtain the codec ID of an MMTF encoded value.

Parameters:

keystr: The key for the potentially encoded value.

Returns:

codecint or None: The codec ID. None if the value is not encoded.

get_length(key)¶

Obtain the length of an MMTF encoded value.

Parameters:

keystr: The key for the potentially encoded value.

Returns:

codecint or None: The length of the bytes array. None if the value is not encoded.

get_param(key)¶

Obtain the parameter of an MMTF encoded value.

Parameters:

keystr: The key for the potentially encoded value.

Returns:

codecint or None: The parameter of the encoded value. None if the value is not encoded.

items() → a set-like object providing a view on D's items¶

keys() → a set-like object providing a view on D's keys¶

pop(k[, d]) → v, remove specified key and return the corresponding value.¶: If key is not found, d is returned if given, otherwise KeyError is raised.

popitem() → (k, v), remove and return some (key, value) pair¶: as a 2-tuple; but raise KeyError if D is empty.

classmethod read(file)¶

Read a MMTF file.

Parameters:

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

Returns:

file_objectMMTFFile: The parsed file.

set_array(key, array, codec, param=0)¶

setdefault(k[, d]) → D.get(k,d), also set D[k]=d if k not in D¶

update([E, ]**F) → None. Update D from mapping/iterable E and F.¶: If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v