cgexplore.analysis.ShapeMeasure

class cgexplore.analysis.ShapeMeasure(output_dir, shape_path, shape_string=None)

Bases: object

Uses Shape to calculate the shape of coordinates.

Shape: http://www.ee.ub.edu/

Methods

calculate	Calculate shape measures for a molecule.
calculate_from_centroids	Calculate shape from the centroids of building blocks.
fill_position_matrix_molecule	Make position matrix from filtering molecule based on element.
get_shape_molecule_byelements	Get molecule to analyse by filtering by element.
reference_shape_dict	Reference shapes as dictionary.

Parameters:

• output_dir (Path | str)

• shape_path (Path | str)

• shape_string (str | None)

calculate(molecule)

Calculate shape measures for a molecule.

Parameters:

molecule (Molecule)

Return type:

dict

calculate_from_centroids(constructed_molecule, target_atmnums)

Calculate shape from the centroids of building blocks.

Currently not implemented well.

Parameters:

• constructed_molecule (ConstructedMolecule)

• target_atmnums (Sequence[int])

Return type:

dict

fill_position_matrix_molecule(molecule, elements, old_position_matrix)

Make position matrix from filtering molecule based on element.

Parameters:

• molecule (Molecule)

• elements (str | Sequence[str])

• old_position_matrix (ndarray)

Return type:

tuple[list, list]

get_shape_molecule_byelements(molecule, elements, expected_points)

Get molecule to analyse by filtering by element.

Parameters:

• molecule (Molecule)

• elements (str | Sequence[str])

• expected_points (int)

Return type:

Molecule | None

reference_shape_dict()

Reference shapes as dictionary.

Return type:

dict[str, dict]