molsysmt.topology.get_dihedral_quartets#

molsysmt.topology.get_dihedral_quartets(molecular_system, with_blocks=False, selection='all', syntax='MolSysMT', **kwargs)[source]#

Finding atom quartets that define standard dihedral angles.

Parameters:

  • molecular_system (molecular system) – Input system.

  • with_blocks (bool, default False) – If True, also return covalent blocks after severing the central bond.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atom selection to restrict the search.

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

  • **kwargs – Flags indicating which dihedrals to compute (e.g., phi=True, psi=True, chi1=True, …).

Returns:

  • list – Quartets of atom indices for the requested dihedrals (list of lists).

  • list, optional – If with_blocks=True, covalent blocks per quartet after removing the central bond.

Notes

  • Uses get_covalent_chains to assemble quartets for each requested dihedral type.

Added in version 1.0.0.