quick pyplot of dihedrals with colors

import ase
from ase import io
import os,time
import numpy as np
import itertools
import matplotlib.pyplot as plt
import matplotlib

fl=os.popen("ls *.pdb").read().split()[0]
mol=io.read(fl)
mol.set_pbc(True)
nat=len(mol.numbers)
radii=covalent_radii[mol.numbers]

dm=[[7, 8, 96, 95], [7, 6, 9, 13], [19, 20, 84, 83], [83, 82, 85, 89], [159, 160, 248, 247], [159, 158, 161, 165], [171, 172, 236, 235], [235, 234, 237, 241]]

Ds=[]

for ifl,fl in enumerate(os.popen("ls *.pdb").read().split()):
	mol=io.read(fl)
	mol.set_pbc(True)
	d2s=[]
	for i in dm:
		imol=mol[i]
		if (imol.get_all_distances()==imol.get_all_distances(mic=True)).all():
			d2s.append(mol.get_dihedral(i))
		else:
			for iat in range(3):
				for idir in range(3):
					d=imol.positions[iat+1]-imol.positions[0]
					if (d[idir]>imol.cell[idir,idir]/2.):
						imol.positions[iat+1]-=imol.cell[idir]
					if (d[idir]<-imol.cell[idir,idir]/2.):
						imol.positions[iat+1]+=imol.cell[idir]
			d2s.append(imol.get_dihedral([0,1,2,3]))
	Ds.append(d2s)

Ds=np.array(Ds)*180./np.pi

from copy import deepcopy

thresh=250.
D2=deepcopy(Ds)
for i in range(len(Ds[0])):
	iwrap=0
	for j in range(len(Ds)-1):
		if ((Ds[j+1,i]+iwrap*360-D2[j,i])>thresh):
			iwrap-=1
		elif ((Ds[j+1,i]+iwrap*360-D2[j,i])<-thresh):
			iwrap+=1
		D2[j+1,i]+=iwrap*360.0


fig,ax1=plt.subplots(1,1,sharex=True,figsize=(18,10))

ld=float(len(Ds[0]))
for i in range(int(ld)):
	plt.plot(np.arange(200),D2[:,i],label="Dihedral_"+str(i),color=matplotlib.cm.hsv(float(i)/ld))
plt.legend()
plt.xlabel("Timestep")
plt.ylabel("Dihedral angle")
plt.xkcd()
plt.savefig("dih_vs_time.png")