moleculekit.pdbx.writer.BinaryCifWriter module#
- class moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifEncoders(defaultStringEncoding='utf-8', storeStringsAsBytes=False, useFloat64=False)#
Bases:
objectColumn-oriented Binary CIF encoders implementing StringArray, ByteArray, IntegerPacking, Delta, RunLength, and FixedPoint encoders from the BinaryCIF specification described in molstar/BinaryCIF
- byteArrayEncoderTyped(colTypedDataList, dataType)#
- deltaEncoderTyped(colTypedDataList, minLen=40)#
- encode(colDataList, encodingTypeList, dataType)#
- encodeWithMask(colDataList, colMaskList, encodingType)#
- floatArrayMaskedEncoder(colDataList, colMaskList)#
- getMask(colDataList)#
Return per-row mask: 0 = present, 1 = ‘.’, 2 = ‘?’/None. None if no mask needed.
- intArrayMaskedEncoder(colDataList, colMaskList)#
- integerPackingEncoderTyped(colTypedDataList)#
- runLengthEncoderTyped(colTypedDataList, minLen=40)#
- stringArrayMaskedEncoder(colDataList, colMaskList)#
- class moleculekit.pdbx.writer.BinaryCifWriter.BinaryCifWriter(typeHints=None, storeStringsAsBytes=False, defaultStringEncoding='utf-8', useFloat64=False)#
Bases:
objectWriter for the binary CIF format.
Type hints are supplied explicitly:
- typeHints = {
“atom_site”: {“id”: “integer”, “Cartn_x”: “float”, …}, …
}
Attributes not present in typeHints[category] default to “string”.
- serialize(filePathOrFileObj, containerList)#
Serialize containerList to BCIF.
filePathOrFileObj may be a filesystem path or any binary file-like object (anything with a write method). Passing a file object lets callers write directly into wrappers like gzip.open(…) without materializing an intermediate file.