shnitsel._accessors#

Attributes#

DATASET_ACCESSOR_NAME

DATAARRAY_ACCESSOR_NAME

DATATREE_ACCESSOR_NAME

Classes#

ShnitselAccessor

DAManualAccessor

DSManualAccessor

Module Contents#

DATASET_ACCESSOR_NAME = 'st'#
DATAARRAY_ACCESSOR_NAME = 'st'#
DATATREE_ACCESSOR_NAME = 'st'#
class ShnitselAccessor(obj)#
_obj: xarray.DataArray | xarray.Dataset#
_methods: list#
_method_needs#
suitable = []#
unsuitable#
_reasons_unavailable(met)#
_repr_html_()#
_ipython_key_completions_()#

Provide method for the key-autocompletions in IPython. See https://ipython.readthedocs.io/en/stable/config/integrating.html#tab-completion For the details.

Return type:

list[str]

class DAManualAccessor(obj)#

Bases: ShnitselAccessor

class DSManualAccessor(obj)#

Bases: ShnitselAccessor

struc_sel(default_selection=None, to2D=True, frame_index=0)#

Create an initial StructureSelection object from a dataset using the entire structural information in it.

Parameters:

  • (xr.Dataset) (frame) – Should only represent a single frame of data (i.e. no ‘frame’ dimension or of zero-size).

  • (Sequence[FeatureLevelOptions] (default_selection) – List of features to activate as selected by default. Defaults to [ ‘atoms’, ‘bonds’, ].

  • optional) – List of features to activate as selected by default. Defaults to [ ‘atoms’, ‘bonds’, ].

  • (bool (to2D) – Flag to control whether a mol representation is converted to a 2d projection before use for visualization.

  • optional) – Flag to control whether a mol representation is converted to a 2d projection before use for visualization.

  • frame_index (int) – Used to select a single frame (using .isel()) if an object containing multiple frames is provided; by default, the first frame is used.

  • default_selection (Sequence[shnitsel.filtering.structure_selection.FeatureLevelOptions] | None)

  • to2D (bool)

Raises:

ValueError – If no structural information could be extracted from the dataset

Returns:

A structure selection object initially covering all atoms and structural features.

Return type:

StructureSelection

Notes

The dataset (single frame) to extract the structure information out of must have at least an atXYZ variable and a atom dimension. Ideally, an atom coordinate for feature selection is also provided.