Align principal axes#

Aligning the principal inertia or geometric axes of a molecular system over reference coordinate axes.

The function molsysmt.structure.align_principal_axes() rotates a molecular system so that its principal axes of inertia (or geometric axes) align with a specified target orthonormal coordinate basis.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.structure.align_principal_axes().

Basic usage#

Let’s demonstrate principal axes alignment using a POPC lipid molecule:

import molsysmt as msm
import numpy as np

crd = msm.systems['POPC']['popc.crd']
psf = msm.systems['POPC']['popc.psf']
molsys = msm.convert([crd, psf], to_form='molsysmt.MolSys')

Note

Demo Systems Catalog

This tutorial uses demonstration datasets provided by MolSysMT. To explore the full catalog of bundled systems, forms, and file paths, visit the Demo Systems guide.

We inspect the principal axes of inertia and their principal moments before alignment using molsysmt.structure.get_principal_axes():

axes, momenta = msm.structure.get_principal_axes(molsys)

for ii in range(3):
    print(f'Axis {ii}: {axes[0, ii]} | Moment: {momenta[0, ii]:.2f}')

Axis 0: [-0.09213962  0.02624376  0.9954002 ] | Moment: 13.38
Axis 1: [0.56239734 0.82631277 0.03027277] | Moment: 73.68
Axis 2: [-0.82171742  0.56259975 -0.09089556] | Moment: 78.33

Now we align the principal axes to the canonical Cartesian basis \([[1,0,0], [0,1,0], [0,0,1]]\):

molsys_aligned = msm.structure.align_principal_axes(molsys, axes=[[1,0,0], [0,1,0], [0,0,1]])

We verify that the principal axes of the aligned system match the canonical Cartesian directions:

axes_aligned, momenta_aligned = msm.structure.get_principal_axes(molsys_aligned)

for ii in range(3):
    print(f'Aligned Axis {ii}: {axes_aligned[0, ii]}')

Aligned Axis 0: [ 1.00000000e+00 -4.52971253e-16 -4.35450667e-16]
Aligned Axis 1: [4.52971253e-16 1.00000000e+00 8.88178420e-16]
Aligned Axis 2: [ 4.35450667e-16 -8.32667268e-16  1.00000000e+00]

Aligning macromolecular coordinates along target spatial axes#

We can similarly align globular protein structures, such as chicken villin HP35, and visualize the aligned system in 3D:

protein = msm.convert(msm.systems['chicken villin HP35']['chicken_villin_HP35.h5msm'])
protein_aligned = msm.structure.align_principal_axes(protein, axes=[[1,0,0], [0,1,0], [0,0,1]])

msm.view(protein_aligned)