%load_ext autoreload
%autoreload 2

import molsysmt as msm
import numpy as np
import matplotlib.pyplot as plt

Center

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

msm.info(molecular_system)

form	n_atoms	n_groups	n_components	n_chains	n_molecules	n_entities	n_peptides	n_structures
molsysmt.MolSys	62	7	1	1	1	1	1	5000

n_structures = msm.get(molecular_system, n_structures=True)
origin = np.zeros([n_structures, 1, 3])*msm.pyunitwizard.unit('nanometers')

geometric_center = msm.structure.get_center(molecular_system)

plt.plot(geometric_center[:,0,0])
plt.plot(geometric_center[:,0,1])
plt.plot(geometric_center[:,0,2])
plt.show()

/home/diego/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/matplotlib/cbook.py:1345: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
  return np.asarray(x, float)

distance_before = msm.structure.get_distances(molecular_system, center_of_atoms=True, molecular_system_2=origin)

molecular_system = msm.structure.center(molecular_system)

distance_after = msm.structure.get_distances(molecular_system, center_of_atoms=True,
                                             molecular_system_2=origin)

plt.plot(distance_before[:,0,0], label='Before centering')
plt.plot(distance_after[:,0,0], label='After centering')
plt.legend()
plt.show()

/home/diego/Myopt/miniconda3/envs/MolSysMT@uibcdf_3.12/lib/python3.12/site-packages/matplotlib/cbook.py:1345: UnitStrippedWarning: The unit of the quantity is stripped when downcasting to ndarray.
  return np.asarray(x, float)