molsysmt.hbonds.get_donor_atoms

molsysmt.hbonds.get_donor_atoms(molecular_system, selection='all', inclusion_rules=None, exclusion_rules=None, default_inclusion_rules=True, default_exclusion_rules=True, syntax='MolSysMT')

Identify donor atoms (and their hydrogens) for hydrogen-bond detection.

Parameters:

• molecular_system (molecular system) – Input system.

• selection (str, list, tuple or numpy.ndarray, default 'all') – Atom selection to filter candidates.

• inclusion_rules (list of str or None) – Selection rules to include or exclude atoms.

• exclusion_rules (list of str or None) – Selection rules to include or exclude atoms.

• default_inclusion_rules (bool, default True) – Whether to apply built-in donor rules.

• default_exclusion_rules (bool, default True) – Whether to apply built-in donor rules.

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

Returns:

Array of donor–hydrogen pairs (shape (n, 2)).

Return type:

numpy.ndarray