molsysmt.structure.get_dihedral_angles#

molsysmt.structure.get_dihedral_angles(molecular_system, selection='all', dihedral_quartets=None, structure_indices='all', syntax='MolSysMT', pbc=False, use_gpu=None, **kwargs)[source]#

Compute dihedral angles for a set of atom quartets over one or more structures.

Two usage modes are available:

  • Explicit quartets — provide dihedral_quartets as an array of shape (n_quartets, 4) containing the atom indices that define each dihedral.

  • Named backbone/side-chain dihedrals — omit dihedral_quartets and pass keyword arguments such as phi=True, psi=True, omega=True, chi1=True, etc. The required quartets are then obtained from molsysmt.topology.get_dihedral_quartets for the atoms in selection. When more than one named type is requested the function returns a list of arrays, one per type.

Angles are computed in the minimum-image convention when pbc=True and the system has a periodic box. Results are always returned in the MolSysMT standard angle unit (degrees).

Parameters:

  • molecular_system (molecular system) – Input system in any form supported by MolSysMT.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atom selection used to resolve named dihedral types (ignored when dihedral_quartets is provided explicitly).

  • dihedral_quartets (numpy.ndarray of shape (n_quartets, 4) or None, default None) – Global atom indices for each dihedral quartet. When None, the quartets are built from the named keyword arguments (phi, psi, etc.).

  • structure_indices ('all' or array-like, default 'all') – Frame indices over which the angles are computed.

  • syntax (str, default 'MolSysMT') – Selection syntax used when selection is a string.

  • pbc (bool, default False) – Apply minimum-image convention when the system has a periodic box.

  • **kwargs – Named dihedral angle flags: phi, psi, omega, chi1, chi2, chi3, chi4, chi5. Each must be set to True to include that dihedral type.

Returns:

  • quantity or list of quantity – PyUnitWizard angle quantity of shape (n_structures, n_quartets) in the standard angle unit (degrees). When more than one named dihedral type is requested, a list of such quantities is returned — one per type, in the order the kwargs were provided.

  • .. versionadded:: 1.0.0

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