molsysmt.structure.get_minimum_distances#

molsysmt.structure.get_minimum_distances(molecular_system, selection='all', center_of_atoms=False, weights=None, as_entity=True, structure_indices='all', molecular_system_2=None, selection_2=None, center_of_atoms_2=False, weights_2=None, as_entity_2=True, structure_indices_2=None, pairs=False, pbc=False, engine='MolSysMT', syntax='MolSysMT', skip_digestion=False)[source]#

Find the minimum pairwise distances between two sets of atoms (or atom-group centers).

Internally calls get_distances and then reduces the full distance matrix by selecting the minimum entry according to the as_entity / as_entity_2 flags.

Parameters:

  • molecular_system (molecular system) – Input system in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – First set of atoms. Nested iterables are treated as groups of atoms when center_of_atoms=True.

  • center_of_atoms (bool, default False) – If True, use the (weighted) centroid of each group in selection instead of individual atom positions.

  • weights (array-like, optional) – Per-atom weights for centroid computation of the first selection.

  • as_entity (bool, default True) – If True, reduce over the entire first set to yield a single minimum per frame. If False, return the minimum partner for each element in the first set.

  • structure_indices ('all' or array-like, default 'all') – Frame indices over which the computation is performed.

  • molecular_system_2 (molecular system or None, default None) – Second system. When None, both selections are drawn from molecular_system.

  • selection_2 (str, list, tuple or numpy.ndarray or None, default None) – Second set of atoms. When None, the minimum is computed within the first selection.

  • center_of_atoms_2 (bool, default False) – If True, use the (weighted) centroid of each group in selection_2.

  • weights_2 (array-like, optional) – Per-atom weights for centroid computation of the second selection.

  • as_entity_2 (bool, default True) – If True, reduce over the entire second set to yield a single minimum per frame. If False, return the minimum partner for each element in the second set.

  • structure_indices_2 ('all', array-like or None, default None) – Frame indices for the second system. When None, the same frames as structure_indices are used.

  • pairs (bool, default False) – If True, selection is interpreted as an array of pre-defined pairs and the minimum is found among those pairs only. Requires both as_entity and as_entity_2 to be True.

  • pbc (bool, default False) – Apply minimum-image convention for periodic boundary conditions.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend used for distance computation.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selections are strings.

  • skip_digestion (bool, default False) – Whether to skip argument digestion (for internal use on trusted hot paths).

Returns:

  • pairs_indices (numpy.ndarray) – Indices of the element pair (within the selection arrays) that achieves the minimum distance. Shape depends on the as_entity flags and whether pairs mode is active.

  • dists (quantity) – PyUnitWizard length quantity of the corresponding minimum distances in the standard length unit (nm).

Raises:

  • ArgumentConflictError – If both as_entity and as_entity_2 are False (use get_distances directly in that case), or if pairs=True with as_entity=False or as_entity_2=False.

  • .. versionadded: – 1.0.0: