def traj_dihedral_calc(ag, dih_list, max_sep, min_sep):
"""
This function loops over a trajectory to calculate the dihedral of a set
of atoms supplied in dih_list
"""
sep_range = max_sep - min_sep
ag_temp = ag
time_range = ag_temp.trajectory.totaltime - ag_temp.trajectory.time
sep_rate = sep_range/time_range
for ts in ag.trajectory:
TPA = ag.selectAtoms("resname TPA")
#Select the 1st, 2nd, 3rd and 4th atoms in the dihedral groups
r1_TPA = TPA[dih_list[:,0]].positions
r2_TPA = TPA[dih_list[:,1]].positions
r3_TPA = TPA[dih_list[:,2]].positions
r4_TPA = TPA[dih_list[:,3]].positions
dih_angle = dihedral_calc(r1_TPA, r2_TPA, r3_TPA, r4_TPA)
dih_angle_deg = np.rad2deg(dih_angle)
#Calculate the separation at the corresponding ts.time step
sep = max_sep - sep_rate * ts.time
dih_file.write(str(ts.time) + " " + str(sep) + " ")
for angle in range(np.shape(dih_angle_deg)[0]):
dih_file.write(str(dih_angle_deg[angle]) + " ")
dih_file.write("\n")
return dih_angle_deg
def single_frame_dihedral_calc(ag, dih_list):
"""
This function calculates the dihedral angles for the list in dih_list for
a single frame of a simulation
"""
TPA = u.selectAtoms("resname TPA")
#Select the 1st, 2nd, 3rd and 4th atoms in the dihedral groups
r1_TPA = TPA[dih_list[:,0]].positions
r2_TPA = TPA[dih_list[:,1]].positions
r3_TPA = TPA[dih_list[:,2]].positions
r4_TPA = TPA[dih_list[:,3]].positions
dih_angle = dihedral_calc(r1_TPA, r2_TPA, r3_TPA, r4_TPA)
dih_angle_deg = np.rad2deg(dih_angle)
for angle in range(np.shape(dih_angle_deg)[0]):
dih_file.write(str(dih_angle_deg[angle]) + " ")
dih_file.write("\n")
return dih_angle_deg