biotite.structure.io.pdbx.CIFFile

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

Bases: _Component, File, MutableMapping

This class represents a CIF file.

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

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

Notes

The content of CIF files are lazily deserialized: When reading the file only the line positions of all blocks are indexed. The time consuming deserialization of a block/category is only performed when accessed. The deserialized CIFBlock/CIFCategory objects are cached for subsequent accesses.

Examples

Read a CIF file and access its content:

>>> import os.path
>>> file = CIFFile.read(os.path.join(path_to_structures, "1l2y.cif"))
>>> 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 CIF file and write it to disk:

>>> category = CIFCategory(
...     {"some_column": "some_value", "another_column": "another_value"}
... )
>>> block = CIFBlock({"some_category": category, "another_category": category})
>>> file = CIFFile({"some_block": block, "another_block": block})
>>> print(file.serialize())
data_some_block
#
_some_category.some_column      some_value
_some_category.another_column   another_value
#
_another_category.some_column      some_value
_another_category.another_column   another_value
#
data_another_block
#
_some_category.some_column      some_value
_some_category.another_column   another_value
#
_another_category.some_column      some_value
_another_category.another_column   another_value
#
>>> file.write(os.path.join(path_to_directory, "some_file.cif"))
Attributes
blockCIFBlock

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

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

Create a deep copy of this object.

Returns
copy

A copy of this object.

static deserialize(text)

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.

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

Parameters
filefile-like object or str

The file to be read. Alternatively a file path can be supplied.

Returns
file_objectCIFFile

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.

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

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

values() → an object providing a view on D's values
write(file)

Write the contents of this object into a CIF file.

Parameters
filefile-like object or str

The file to be written to. Alternatively a file path can be supplied.