molsysmt.structure.set_dihedral_angles#

molsysmt.structure.set_dihedral_angles(molecular_system, dihedral_quartets=None, angles=None, blocks=None, structure_indices='all', pbc=True, in_place=False, engine='MolSysMT')[source]#

Set dihedral angles to specified target values by rotating covalent blocks.

For each dihedral quartet (i, j, k, l), the function determines which atoms form a covalently connected block on the side of atom l after the bond j-k is removed. That block is then rotated about the j-k axis so that the dihedral angle reaches the target value.

When pbc=True and the system has a periodic box the minimum-image dihedral kernel is used; otherwise the standard (non-periodic) kernel is applied.

Parameters:

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

  • dihedral_quartets (numpy.ndarray of shape (n_quartets, 4)) – Global atom indices defining each dihedral angle to be set. Each row contains four atom indices [i, j, k, l].

  • angles (quantity) – Target dihedral angle values as a PyUnitWizard angle quantity. The array must be compatible with shape (n_structures, n_quartets). Values are internally converted to radians.

  • blocks (list of sets or None, default None) – Pre-computed covalent blocks (one per quartet) used to determine which atoms move. When None, the blocks are computed on-the-fly for every quartet by calling molsysmt.topology.get_covalent_blocks with the relevant bond removed. Providing pre-computed blocks avoids redundant topology traversals when calling this function in a loop.

  • structure_indices ('all' or array-like, default 'all') – Frame indices over which the operation is performed.

  • pbc (bool, default True) – Use the minimum-image dihedral kernel when the system has a periodic box.

  • in_place (bool, default False) – If True the molecular system is modified in-place and None is returned. If False a new copy is returned with the updated coordinates.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend used for the dihedral rotation kernels.

Returns:

A new molecular system with the updated dihedral angles when in_place=False; None when in_place=True.

Return type:

molecular system or None

Raises:

  • NotImplementedMethodError – If an unsupported engine is requested.

  • .. versionadded: – 1.0.0:

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