compress

biotite.structure.io.pdbx.compress(data, float_tolerance=1e-06)

Try to reduce the size of a BinaryCIF file (or block, category, etc.) by testing different data encodings for each data array and selecting the one, which results in the smallest size.

Parameters:

dataBinaryCIFFile or BinaryCIFBlock or BinaryCIFCategory or BinaryCIFColumn or BinaryCIFData

The data to compress.

Returns:

compressed_fileBinaryCIFFile or BinaryCIFBlock or BinaryCIFCategory or BinaryCIFColumn or BinaryCIFData

The compressed data with the same type as the input data. If no improved compression is found for a BinaryCIFData array, the input data is kept. Hence, the return value is no deep copy of the input data.

float_tolerancefloat, optional

The relative error that is accepted when compressing floating point numbers.

Examples

>>> from io import BytesIO
>>> pdbx_file = BinaryCIFFile()
>>> set_structure(pdbx_file, atom_array_stack)
>>> # Write uncompressed file
>>> uncompressed_file = BytesIO()
>>> pdbx_file.write(uncompressed_file)
>>> _ = uncompressed_file.seek(0)
>>> print(f"{len(uncompressed_file.read()) // 1000} KB")
927 KB
>>> # Write compressed file
>>> pdbx_file = compress(pdbx_file)
>>> compressed_file = BytesIO()
>>> pdbx_file.write(compressed_file)
>>> _ = compressed_file.seek(0)
>>> print(f"{len(compressed_file.read()) // 1000} KB")
111 KB