import molsysmt as msm
from molsysmt import pyunitwizard as puw
import numpy as np
import matplotlib.pyplot as plt

Principal component analysis

molecular_system = msm.systems['pentalanine']['traj_pentalanine.h5']
molecular_system = msm.convert(molecular_system, to_form='molsysmt.MolSys')

pcs, sigmas = msm.structure.principal_component_analysis(molecular_system, selection='atom_name=="CA"')

sigmas

array([-7.61673223e+00, -2.40353497e+00, -7.07258185e-01, -5.66336274e-01,
       -4.55056633e-01, -7.10380242e-03, -3.47446577e-03,  1.28211399e-03,
        1.99369789e-03,  4.33715991e-03,  3.91734124e-02,  4.61545377e-01,
        4.96569155e-01,  8.32111142e-01,  9.15973936e-01])