topology

Molecular mechanics topology primitives.

import mlx_atomistic.topology

Classes

Topology

class Topology
    def __init__(n_atoms: int, bonds: object = (), angles: object = (), dihedrals: object = (), impropers: object = (), exclusions: object = (), partial_charges: object | None = None, one_four_pairs: object = (), nonbonded_exception_pairs: object = (), exclude_bonds: bool = True, nonbonded_cutoff: float | None = None, eager_nonbonded_pair_limit: int | None = DEFAULT_EAGER_NONBONDED_PAIR_LIMIT, virtual_sites: object = (), virtual_site_types: object = ())

Programmatic molecular mechanics topology.

Parameters

Name	Type	Default	Description
n_atoms	int
bonds	object	()
angles	object	()
dihedrals	object	()
impropers	object	()
exclusions	object	()
partial_charges	object | None	None
one_four_pairs	object	()
nonbonded_exception_pairs	object	()
exclude_bonds	bool	True
nonbonded_cutoff	float | None	None
eager_nonbonded_pair_limit	int | None	DEFAULT_EAGER_NONBONDED_PAIR_LIMIT
virtual_sites	object	()
virtual_site_types	object	()

Properties

• exclusion_set frozenset[tuple[int, int]] — Excluded nonbonded pairs as normalized Python pairs.
• nonbonded_build_report dict[str, int | float | str | None] — Compact report for topology nonbonded pair handling.
• nonbonded_pair_count int — Number of non-excluded full-system nonbonded pairs.
• nonbonded_pair_policy str — Whether full nonbonded pairs were eagerly materialized or deferred.
• one_four_set frozenset[tuple[int, int]] — 1-4 scaled nonbonded pairs as normalized Python pairs.

Methods

from_sequences

def from_sequences(*, n_atoms: int, bonds: Sequence[Sequence[int]] = (), angles: Sequence[Sequence[int]] = (), dihedrals: Sequence[Sequence[int]] = (), impropers: Sequence[Sequence[int]] = (), exclusions: Sequence[Sequence[int]] = (), partial_charges: Sequence[float] | None = None, one_four_pairs: Sequence[Sequence[int]] | None = None, nonbonded_exception_pairs: Sequence[Sequence[int]] = (), exclude_bonds: bool = True, nonbonded_cutoff: float | None = None, eager_nonbonded_pair_limit: int | None = DEFAULT_EAGER_NONBONDED_PAIR_LIMIT, virtual_sites: Sequence[object] = (), virtual_site_types: Sequence[str] = ()) -> Topology

Create a topology from Python sequences.

Parameters

Name	Type	Default	Description
n_atoms	int
bonds	Sequence[Sequence[int]]	()
angles	Sequence[Sequence[int]]	()
dihedrals	Sequence[Sequence[int]]	()
impropers	Sequence[Sequence[int]]	()
exclusions	Sequence[Sequence[int]]	()
partial_charges	Sequence[float] | None	None
one_four_pairs	Sequence[Sequence[int]] | None	None
nonbonded_exception_pairs	Sequence[Sequence[int]]	()
exclude_bonds	bool	True
nonbonded_cutoff	float | None	None
eager_nonbonded_pair_limit	int | None	DEFAULT_EAGER_NONBONDED_PAIR_LIMIT
virtual_sites	Sequence[object]	()
virtual_site_types	Sequence[str]	()

Returns

• Topology

nonbonded_pair_scales

def nonbonded_pair_scales(*, one_four_scale: float = 1.0) -> mx.array

Return cached per-pair 1-4 scaling factors for all nonbonded pairs.

Parameters

Name	Type	Default	Description
one_four_scale	float	1.0

Returns

• mx.array

nonbonded_pairs

def nonbonded_pairs(pairs = None) -> mx.array

Return nonbonded pairs with topology exclusions removed.

Parameters

Name	Type	Default	Description
pairs		None

Returns

• mx.array

pair_scales

def pair_scales(pairs, *, one_four_scale: float = 1.0) -> mx.array

Return per-pair 1-4 scaling factors.

Parameters

Name	Type	Default	Description
pairs
one_four_scale	float	1.0

Returns

• mx.array