`RunLengthEncoding`#

class biotite.structure.io.pdbx.RunLengthEncoding(src_size: ... = None, src_type: ... = None)[source]#

Bases: Encoding

Encoding that compresses runs of equal values into pairs of (value, run length).

Parameters:

src_sizeint, optional: The size of the array to be encoded. If omitted, the size is determined from the data the first time encode() is called.
src_typedtype or TypeCode, optional: The data type of the array to be encoded. Either a NumPy dtype or a BinaryCIF type code is accepted. The dtype must be a integer type. If omitted, the data type is taken from the data the first time encode() is called.

Examples

>>> data = np.array([1, 1, 1, 5, 3, 3])
>>> print(data)
[1 1 1 5 3 3]
>>> encoded = RunLengthEncoding().encode(data)
>>> print(encoded)
[1 3 5 1 3 2]
>>> # Emphasize the the pairs
>>> print(encoded.reshape(-1, 2))
[[1 3]
 [5 1]
 [3 2]]

Attributes:

src_sizeint
src_typeTypeCode

decode(data)#

Apply the inverse of this encoding to the given data.

Parameters:

datandarray or bytes: The data to be decoded.

Returns:

decoded_datandarray: The decoded data.

classmethod 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.

encode(data)#

Apply this encoding to the given data.

Parameters:

datandarray: The data to be encoded.

Returns:

encoded_datandarray or bytes: The encoded data.

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.

Gallery#

BinaryCIF as trajectory format

RunLengthEncoding#

Gallery#

`RunLengthEncoding`#