molsysmt.hbonds.get_buch_hbonds

molsysmt.hbonds.get_buch_hbonds(molecular_system, selection='all', acceptors=None, donors=None, structure_indices='all', molecular_system_2=None, selection_2=None, acceptors_2=None, donors_2=None, structure_indices_2=None, distance_threshold='2.3 angstroms', pbc=True, syntax='MolSysMT', skip_digestion=False)

Calculating hydrogen bonds using the Buch geometric criteria.

Parameters:

• molecular_system (molecular system) – Input system containing potential donors/acceptors.

• selection (str, list, tuple or numpy.ndarray, default 'all') – Atom selection used to derive donors/acceptors (MolSysMT syntax or indices).

• acceptors (array-like or None) – Preselected acceptor/donor atom indices; if None, they are inferred from selection.

• donors (array-like or None) – Preselected acceptor/donor atom indices; if None, they are inferred from selection.

• structure_indices ('all' or array-like, default 'all') – Structures/frames over which to compute.

• molecular_system_2 (molecular system, optional) – Second system for intermolecular H-bonds; if None, uses molecular_system.

• selection_2 (array-like or None) – Counterpart selections/indices for molecular_system_2 when provided.

• acceptors_2 (array-like or None) – Counterpart selections/indices for molecular_system_2 when provided.

• donors_2 (array-like or None) – Counterpart selections/indices for molecular_system_2 when provided.

• structure_indices_2 ('all' or array-like, optional) – Structures for the second system; defaults to structure_indices.

• distance_threshold (quantity or str, default '2.3 angstroms') – Maximum donor–acceptor distance.

• pbc (bool, default True) – Whether to consider periodic boundary conditions.

• syntax (str, default 'MolSysMT') – Selection syntax for string selections.

• skip_digestion (bool, default False) – Whether to skip argument digestion.

Returns:

(atoms, distances) arrays per structure for the detected H-bonds.

Return type:

tuple