molsysmt.hbonds package#
Submodules#
molsysmt.hbonds.get_acceptor_atoms module#
- molsysmt.hbonds.get_acceptor_atoms.get_acceptor_atoms(molecular_system, selection='all', inclusion_rules=None, exclusion_rules=None, default_inclusion_rules=True, default_exclusion_rules=True, syntax='MolSysMT')[source]#
Identify acceptor atoms within a molecular system 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 acceptor rules.
default_exclusion_rules (bool, default True) – Whether to apply built-in acceptor rules.
syntax (str, default 'MolSysMT') – Selection syntax for string rules.
- Returns:
Sorted array of acceptor atom indices.
- Return type:
numpy.ndarray
molsysmt.hbonds.get_buch_hbonds module#
- molsysmt.hbonds.get_buch_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)[source]#
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
molsysmt.hbonds.get_donor_atoms module#
- molsysmt.hbonds.get_donor_atoms.get_donor_atoms(molecular_system, selection='all', inclusion_rules=None, exclusion_rules=None, default_inclusion_rules=True, default_exclusion_rules=True, syntax='MolSysMT')[source]#
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
molsysmt.hbonds.get_luzard_chandler_hbonds module#
- molsysmt.hbonds.get_luzard_chandler_hbonds.get_luzard_chandler_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='3.5 angstroms', angle_threshold='30 degrees', pbc=True, syntax='MolSysMT')[source]#
Calculating hydrogen bonds using the Luzard–Chandler 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 '3.5 angstroms') – Maximum donor–acceptor distance.
angle_threshold (quantity or str, default '30 degrees') – Maximum deviation from linearity (D–H···A); smaller angles are stricter.
pbc (bool, default True) – Whether to consider periodic boundary conditions.
syntax (str, default 'MolSysMT') – Selection syntax for string selections.
- Returns:
(atoms, distances, angles) arrays per structure for the detected H-bonds.
- Return type:
tuple