autofragment.partitioners.qmmm

QM/MM partitioner for multi-level calculations.

This module provides a partitioner specifically designed for QM/MM calculations, including QM region selection, buffer zone generation, and link atom placement.

Example

>>> from autofragment.partitioners.qmmm import QMMMPartitioner, AtomSelection
>>> selection = AtomSelection(atom_indices={0, 1, 2, 3, 4})
>>> partitioner = QMMMPartitioner(qm_selection=selection, buffer_radius=5.0)
>>> system = ChemicalSystem.from_molecules(molecules)
>>> result = partitioner.partition(system)

Classes

AtomSelection(atom_indices)	Select QM region by explicit atom indices.
CombinedSelection(selections[, mode])	Combine multiple selection strategies.
DistanceSelection(center, radius)	Select QM region by distance from a center point.
QMMMPartitioner(qm_selection[, ...])	Partitioner for QM/MM calculations.
QMMMResult(qm_atoms, buffer_atoms, mm_atoms)	Result of QM/MM partitioning.
QMSelection()	Abstract base class for QM region selection strategies.
ResidueSelection([residue_names, ...])	Select QM region by residue name or number.
TopologySelection(seed_atoms[, mode, hops, ...])	Select QM region by topology or nearest-neighbor neighborhood shells.