Analyzing MD simulations

import numpy as np
import matplotlib.pyplot as plt
import chilife as xl

C:\Program Files\Python312\Lib\site-packages\tqdm\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

traj = xl.load_protein('AR1A.pdb', 'AR1A.xtc')
SL = xl.SpinLabel.from_trajectory(traj, 2, spin_atoms=['NN', 'ON'], use_H=True)
print(SL)

Ligand ensemble with 237 members
  Name: 2CYR_from_traj
  Ligand: CYR
  Site: 2
  Dihedral definitions:
    ['N', 'CA', 'CB', 'SG']
    ['CA', 'CB', 'SG', 'S1L']
    ['CB', 'SG', 'S1L', 'C1L']
    ['SG', 'S1L', 'C1L', 'C1R']
    ['S1L', 'C1L', 'C1R', 'C2R']

mosaic = """AABBCC
            .DDEE."""
fig, ax_dict = plt.subplot_mosaic(mosaic, figsize=(10, 5), subplot_kw=dict(projection="polar"))

for i, ax in enumerate(ax_dict.values()):
    ax.hist(np.deg2rad(SL.dihedrals[:, i]), bins=np.linspace(-np.pi, np.pi, 37))
    ax.set_yticklabels([])
    xlab = ["0", "45", "90", "135", r"$\rm\pm180$", "-135", "-90", "-45" ]
    xlab = [x + r"$\degree$" for x in xlab]
    ax.set_xticklabels(xlab)
    ax.tick_params(axis='x', which='major', pad=10)
    ax.set_title(f"$\\rm\\chi_{i + 1}$")
plt.tight_layout()
plt.show()

SL.to_rotlib('CYR', 'Cstom MTSL (R1) rotamer library',
             "An MTSL/R1 rotamer library made with well tempered metadynamics")

prot = xl.fetch('1ubq')

SL = xl.SpinLabel('CYR', 28, prot)
xl.save(prot, SL)