molsysmt.element.group.amino_acid.get_bonded_atom_pairs#

molsysmt.element.group.amino_acid.get_bonded_atom_pairs(group_name, atom_names, atom_indices=None, sorted=True, skip_digestion=False)[source]#

Getting standard intra-group covalent bonded atom pairs for amino acid residues.

Parameters:

  • group_name (str) – Name of the chemical group (residue).

  • atom_names (numpy.ndarray, list, or tuple) – Names of atoms in the group.

  • atom_indices (int, list, tuple, or numpy.ndarray, default=None) – Atom indices (0-based) to include.

  • sorted (bool, default=True) – Whether to sort the returned bonded atom pairs.

  • skip_digestion (bool, default=False) – Whether to skip MolSysMT’s internal argument digestion mechanism.

Returns:

List of bonded atom name pairs.

Return type:

list of tuple of str

Added in version 1.0.0.