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) – Molecular system in any supported MolSysMT format.

  • with_blocks (bool, default=False) – Whether to return the movable atom blocks with each dihedral quartet.

  • selection (str, list, tuple, or numpy.ndarray, default='all') – Selection string or boolean/integer array specifying elements.

  • syntax (str, default='MolSysMT') – Selection syntax used to evaluate selection (e.g., ‘MolSysMT’, ‘MDTraj’).

Returns:

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

  • list, optional – If with_blocks=True, the covalent blocks obtained after removing the central bond of each quartet: one entry per quartet, each a list of sets of atom indices. The two sets of a quartet are the groups of atoms that move apart when that dihedral angle is rotated. This is ragged on purpose and is not a NumPy array.

Notes

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

Added in version 1.0.0.