mlcolvar.data.graph.AtomicNumberTable

class mlcolvar.data.graph.AtomicNumberTable(zs: List[int])

Bases: object

The atomic number table. Used to map between one hot encodings and a given set of actual atomic numbers.

__init__(zs: List[int]) → None

Initializes an atomi number table object

Parameters:

zs (List[int]) – The atomic numbers in this table

Methods

__init__(zs)	Initializes an atomi number table object
from_zs(atomic_numbers)	Build the table from an array atomic numbers.
index_to_symbol(index)	Map the encoding to the atomic symbol
index_to_z(index)	Maps the encoding to the actual atomic number
z_to_index(atomic_number)	Maps an atomic number to the encoding.
zs_to_indices(atomic_numbers)	Maps an array of atomic number to the encodings.

classmethod from_zs(atomic_numbers: Iterable[int]) → AtomicNumberTable

Build the table from an array atomic numbers.

Parameters:

atomic_numbers (Iterable[int]) – The atomic numbers to be used for building the table

index_to_symbol(index: int) → str

Map the encoding to the atomic symbol

Parameters:

index (int) – Index of the encoding to be mapped

index_to_z(index: int) → int

Maps the encoding to the actual atomic number

Parameters:

index (int) – Index of the encoding to be mapped

z_to_index(atomic_number: int) → int

Maps an atomic number to the encoding.

Parameters:

atomic_number (int) – The atomic number to be mapped

zs_to_indices(atomic_numbers: ndarray) → ndarray

Maps an array of atomic number to the encodings.

Parameters:

atomic_numbers (numpy.ndarray) – The atomic numbers to be mapped