graph2mat.AtomicTableWithEdges

class graph2mat.AtomicTableWithEdges(atoms: Sequence[Atom])[source]

Bases: BasisTableWithEdges

Variant of BasisTableWithEdges for the case in which points are atoms.

This class mostly just adds a few aliases to the methods of BasisTableWithEdges by replacing “point” to “atom” in the method names. It also provides some methods to create a table from atomic basis.

See also

BasisTableWithEdges

The class that actually does the work.

Methods

atom_block_pointer(atom_types)

atom_type_to_edge_type(atom_type)

from_basis_dir(basis_dir[, basis_ext, ...])

Generates a table from a directory containing basis files.

from_basis_glob(basis_glob[, no_basis_atoms])

Generates a table from basis files that match a glob pattern.

Attributes

atom_block_shape

atom_block_size

atomic_DM

zs

atoms

file_names

file_contents

basis

basis_convention

types

point_matrix

edge_type

R

basis_size

point_block_shape

point_block_size

edge_block_shape

edge_block_size

edge_type_to_point_types

change_of_basis

change_of_basis_inv

atom_block_pointer(atom_types: Sequence[int])[source]
property atom_block_shape
property atom_block_size
atom_type_to_edge_type(atom_type: ndarray)[source]
property atomic_DM
atoms: List[Atom]
file_contents: List[str] | None
file_names: List[str] | None
classmethod from_basis_dir(basis_dir: str, basis_ext: str = 'ion.xml', no_basis_atoms: dict | None = None) AtomicTableWithEdges[source]

Generates a table from a directory containing basis files.

Parameters:
  • basis_dir – The directory containing the basis files.

  • basis_ext – The extension of the basis files.

classmethod from_basis_glob(basis_glob: str | Generator, no_basis_atoms: dict | None = None) AtomicTableWithEdges[source]

Generates a table from basis files that match a glob pattern.

Parameters:

basis_glob – The glob pattern to match the basis files.

property zs