biotite.structure.io.pdbx.CIFColumn

class biotite.structure.io.pdbx.CIFColumn(data, mask=None)

Bases: object

This class represents a single column in a CIFCategory.

Parameters

dataCIFData or array_like or int or float or str

The data to be stored. If no CIFData is given, the passed argument is coerced into such an object.

maskCIFData or array_like, dtype=int or int

The mask to be stored. If given, the mask indicates whether the data is inapplicable (.) or missing (?) in some rows. The data presence is indicated by values from the MaskValue enum. If no CIFData is given, the passed argument is coerced into such an object. By default, no mask is created.

Examples

>>> print(CIFColumn([1, 2, 3]).as_array())
['1' '2' '3']
>>> mask = [MaskValue.PRESENT, MaskValue.INAPPLICABLE, MaskValue.MISSING]
>>> print(CIFColumn([1, 2, 3], mask).as_array())
['1' '.' '?']
>>> print(CIFColumn([1]).as_item())
1
>>> print(CIFColumn([1], mask=[MaskValue.MISSING]).as_item())
?

Attributes

dataCIFData

The stored data.

maskCIFData

The mask that indicates whether certain data elements are inapplicable or missing. If no mask is present, this attribute is None.

as_array(dtype=<class 'str'>, masked_value=None)

Get the data of this column as an ndarray.

This is a shortcut to get CIFColumn.data.array. Furthermore, the mask is applied to the data.

Parameters

dtypedtype-like, optional

The data type the array should be converted to. By default, a string type is used.

masked_valuestr, optional

The value that should be used for masked elements, i.e. MaskValue.INAPPLICABLE or MaskValue.MISSING. By default, masked elements are converted to '.' or '?' depending on the MaskValue.

as_item()

Get the only item in the data of this column.

If the data is masked as inapplicable or missing, '.' or '?' is returned, respectively. If the data contains more than one item, an exception is raised.

Returns

itemstr

The item in the data.

static subcomponent_class()

static supercomponent_class()