`HierarchyElement`

class openff.toolkit.topology.HierarchyElement(scheme: HierarchyScheme, identifier: tuple[Union[str, int]], atom_indices: Sequence[int])[source]

An element in a metadata hierarchy scheme, such as a residue or chain.

__init__(scheme: HierarchyScheme, identifier: tuple[Union[str, int]], atom_indices: Sequence[int])[source]

Create a new hierarchy element.

Parameters:

scheme – The scheme to which this HierarchyElement belongs
identifier – tuple of metadata values (not keys) that define the uniqueness criteria for this element
atom_indices – The indices of particles in scheme.parent that are in this element

Methods

`__init__`(scheme, identifier, atom_indices)	Create a new hierarchy element.
`atom`(index)	Get the atom with the specified index.
`generate_unique_atom_names`([suffix])	Generate unique atom names from the element symbol and count.
`to_dict`()	Serialize this object to a basic dict of strings and lists of ints.

Attributes

`atoms`	Iterator over the atoms in this hierarchy element.
`has_unique_atom_names`	`True` if the element has unique atom names, `False` otherwise.
`n_atoms`	The number of atoms in this hierarchy element.
`parent`	The parent molecule for this hierarchy element

to_dict() → dict[str, Union[tuple[Union[str, int]], Sequence[int]]][source]: Serialize this object to a basic dict of strings and lists of ints.

property n_atoms: int: The number of atoms in this hierarchy element.

property atoms: Generator[Atom, None, None]: Iterator over the atoms in this hierarchy element.

atom(index: int) → Atom[source]: Get the atom with the specified index.

property parent: Molecule | FrozenMolecule | _SimpleMolecule: The parent molecule for this hierarchy element

property has_unique_atom_names: bool: True if the element has unique atom names, False otherwise.

generate_unique_atom_names(suffix: str = 'x')[source]

Generate unique atom names from the element symbol and count.

Names are generated from the elemental symbol and the number of times that element is found in the hierarchy element. The character ‘x’ is appended to these generated names to reduce the odds that they clash with an atom name or type imported from another source. For example, generated atom names might begin ‘C1x’, ‘H1x’, ‘O1x’, ‘C2x’, etc.

Parameters:: suffix – Optional suffix added to atom names. Assists in denoting molecule types