`BinaryCIFFile`#

class biotite.structure.io.pdbx.BinaryCIFFile(blocks=None)[source]#

Bases: File, _HierarchicalContainer

This class represents a BinaryCIF file.

The categories of the file can be accessed and modified like a dictionary. The values are BinaryCIFBlock objects.

To parse or write a structure from/to a BinaryCIFFile object, use the high-level get_structure() or set_structure() function respectively.

Parameters:

blocksdict (str -> BinaryCIFBlock), optional: The initial blocks of the file. Maps the block names to the corresponding BinaryCIFBlock objects. By default no initial blocks are added.

Attributes:

blockBinaryCIFBlock: The sole block of the file. If the file contains multiple blocks, an exception is raised.

Notes

The content of BinaryCIF files are lazily deserialized: Only when a column is accessed, the time consuming data decoding is performed. The decoded BinaryCIFBlock/BinaryCIFCategory objects are cached for subsequent accesses.

Examples

Read a BinaryCIF file and access its content:

>>> import os.path
>>> file = BinaryCIFFile.read(os.path.join(path_to_structures, "1l2y.bcif"))
>>> print(file["1L2Y"]["citation_author"]["name"].as_array())
['Neidigh, J.W.' 'Fesinmeyer, R.M.' 'Andersen, N.H.']
>>> # Access the only block in the file
>>> print(file.block["entity"]["pdbx_description"].as_item())
TC5b

Create a BinaryCIF file and write it to disk:

>>> category = BinaryCIFCategory({"some_column": "some_value"})
>>> block = BinaryCIFBlock({"some_category": category})
>>> file = BinaryCIFFile({"some_block": block})
>>> file.write(os.path.join(path_to_directory, "some_file.bcif"))

copy()#

Create a deep copy of this object.

Returns:

copy: A copy of this object.

static deserialize(content)#

Create this component by deserializing the given content.

Parameters:

contentstr or dict: The content to be deserialized. The type of this parameter depends on the file format. In case of CIF files, this is the text of the lines that represent this component. In case of BinaryCIF files, this is a dictionary parsed from the MessagePack data.

classmethod read(file)#

Read a BinaryCIF file.

Parameters:

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

Returns:

file_objectBinaryCIFFile: The parsed file.

serialize()#

Convert this component into a Python object that can be written to a file.

Returns:

contentstr or dict: The content to be serialized. The type of this return value depends on the file format. In case of CIF files, this is the text of the lines that represent this component. In case of BinaryCIF files, this is a dictionary that can be encoded into MessagePack.

static subcomponent_class()#

Get the class of the components that are stored in this component.

Returns:

subcomponent_classtype: The class of the subcomponent. If this component already represents the lowest level, i.e. it does not contain subcomponents, None is returned.

static supercomponent_class()#

Get the class of the component that contains this component.

Returns:

supercomponent_classtype: The class of the supercomponent. If this component present already the highest level, i.e. it is not contained in another component, None is returned.

write(file)#

Write contents into a BinaryCIF file.

Parameters: