import pytraj as pt
import numpy as np
traj = pt.iterload("RAN.rst7", "RAN.parm7")
print(traj.n_atoms, traj.top.n_residues)
print(pt.calc_chin(traj))
t0 = traj[:1]
deg_ene = []
flist = []
for deg in range(-180, 180, 5):
pt._rotate_dih(t0, dihtype='chin', deg=deg, resid='1')
flist.append(t0[0].copy())
en = pt.energy_decomposition(flist,
top=traj.top,
igb=8,
parm='./RAN.parm7')['dihedral']
chin = pt.calc_chin(flist, top=traj.top).values
en = en - en.min()
from matplotlib import pyplot as plt
plt.plot(chin, en, '--bo')
plt.show()
#!/usr/bin/env python
import pytraj as pt
traj = pt.iterload('./RAN.rst7', './RAN.parm7')
t0 = traj[:]
flist = []
for deg in range(-180, 175, 5):
pt._rotate_dih(t0, resid='1', dihtype='chin', deg=deg)
flist.append(t0[0].copy())
print(pt.calc_chin(flist, top=t0.top))
pt.write_traj('combined_traj.nc', flist, top=t0.top)
import pytraj as pt # load DNA structure # calculate glycosidic torsion angle trajin = "../tests/data/Test_NAstruct/adh026.3.crd" parm = "../tests/data/Test_NAstruct/adh026.3.top" traj = pt.iterload(trajin, parm) print(pt.calc_chin(traj)) print(pt.calc_chin(traj, resrange=range(3, 21, 3)))