molsysmt.structure.get_principal_axes#

molsysmt.structure.get_principal_axes(molecular_system, selection='all', structure_indices='all', weights=None, principal_axes_type='inertia', syntax='MolSysMT', engine='MolSysMT', use_gpu=None, skip_digestion=False)[source]#

Computing principal axes for a selection of atoms.

Parameters:

  • molecular_system (molecular system) – Input system.

  • selection (str, list, tuple or numpy.ndarray, default 'all') – Atoms used for axis computation.

  • structure_indices ('all' or array-like, default 'all') – Structures/frames to evaluate.

  • weights (array-like, quantity, 'masses' or None, default None) – Non-negative weights per atom. None assigns unit weight to every atom. Use 'masses' for physical principal inertia axes.

  • principal_axes_type ({'inertia', 'geometric'}, default 'inertia') – Kind of principal axes to compute.

  • syntax (str, default 'MolSysMT') – Selection syntax when using strings.

  • engine ({'MolSysMT'}, default 'MolSysMT') – Backend.

  • use_gpu (bool or 'auto', optional) – Whether to use a supported GPU backend.

  • skip_digestion (bool, default False) – Whether to skip argument digestion.

Returns:

(axes, moments) where axes has shape (n_structures, 3, 3) and moments has shape (n_structures, 3). Moments are geometric variances or inertia moments, depending on principal_axes_type.

Return type:

tuple

Raises:

  • ArgumentError – If the atom or frame selection is empty, or weights are invalid.

  • ArgumentLengthError – If the number of weights does not match the selected atoms.

  • NotImplementedMethodError – If the engine is unsupported.

Notes

Axes are returned as rows, ordered by ascending eigenvalue, and form a right-handed orthonormal basis. Individual axis signs are mathematically arbitrary. Degenerate eigenvalues define a subspace rather than unique individual axes.

See also

molsysmt.structure.align_principal_axes()

Align coordinates to a target principal-axis basis.

molsysmt.structure.get_center()

Compute geometric or weighted centers.

Examples

>>> import molsysmt as msm
>>> molsys = msm.systems['alanine dipeptide']['alanine_dipeptide.h5msm']
>>> axes, moments = msm.structure.get_principal_axes(
...     molsys, structure_indices=0, weights='masses'
... )
>>> axes.shape, moments.shape
((1, 3, 3), (1, 3))
>>> round(float(np.linalg.det(axes[0])), 12)
1.0

Tutorial with more examples

See Getting principal axes.

Added in version 1.0.0.

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