%load_ext autoreload
%autoreload 2

import molsysmt as msm

Align principal axes

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])

msm.info(molsys)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_lipids	n_structures
molsysmt.MolSys	134	1	1	1	1	1	1	1

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

for ii in range(3):
    print(axes[0,ii], momenta[0,ii])

[ 0.09213962 -0.02624376 -0.9954002 ] 13.378581090770417
[0.56239734 0.82631277 0.03027277] 73.67866342245162
[-0.82171742  0.56259975 -0.09089556] 78.32952437971095

msm.view(molsys, standard=False)

molsys_2 = msm.structure.align_principal_axes(molsys, axes=[[1,0,0],[0,1,0],[0,0,1]])

axes, momenta = msm.structure.get_principal_axes(molsys_2)

for ii in range(3):
    print(axes[0,ii], momenta[0,ii])

[1.00000000e+00 2.89062648e-16 9.82862152e-17] 13.378581090770416
[-2.89062648e-16  1.00000000e+00 -1.77635684e-15] 73.67866342245162
[-9.82862152e-17  1.77635684e-15  1.00000000e+00] 78.32952437971093

msm.view(molsys_2, standard=False)