biotite.structure.io.pdbx.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.