matplotlib example hacky rgyr and rdist (snippet)

Python matplotlib example 'hacky rgyr and rdist'

Modules used in program:

• import seaborn as sns, numpy as np
• import numpy.linalg
• import seaborn as sns
• import numpy as np
• import numpy.linalg
• import MDAnalysis as mda
• import numpy.linalg
• import numpy as np
• import matplotlib.pyplot as plt
• import matplotlib
• import MDAnalysis as mda
• import itertools
• import sys
• import csv
• import argparse

python hacky rgyr and rdist

Python matplotlib example: hacky rgyr and rdist

#!/usr/bin/env python
# coding: utf-8

# In[1]:


import argparse
import csv
import sys

import itertools
import MDAnalysis as mda

import matplotlib
matplotlib.use('Agg')  # noqa
get_ipython().run_line_magic('matplotlib', 'inline')
import matplotlib.pyplot as plt

import numpy as np
import numpy.linalg
from MDAnalysis.analysis.dihedrals import Ramachandran
import MDAnalysis as mda
from MDAnalysis.lib.distances import calc_dihedrals


import numpy.linalg
import numpy as np

import seaborn as sns
from collections import namedtuple


# In[2]:


import numpy.linalg

pdb = "step3_charmm2omm.pdb"
dcd = "step5_1.dcd"
rgyr_selection = 'segid PROF and backbone'

u = mda.Universe(pdb, dcd)        # always start with a Universe
nterm = u.PROF.atoms.N[0]   # can access structure via segid (s4AKE) and atom name
cterm = u.PROF.atoms.C[-1]  # ... takes the last atom named 'C'
bb = u.select_atoms('segid PROF and backbone')  # a selection (a AtomGroup)
Rgyr = []
D = []
for ts in u.trajectory:     # iterate through all frames
  r = cterm.position - nterm.position # end-to-end vector from atom positions
  d = numpy.linalg.norm(r)  # end-to-end distance
  rgyr = bb.radius_of_gyration()  # method of a AtomGroup; updates with each frame
  Rgyr.append((u.trajectory.time, rgyr))
  D.append((u.trajectory.time, d))
  #print("frame = %d: d = %f Angstroem, Rgyr = %f Angstroem" % (ts.frame, d, rgyr))
Rgyr = np.array(Rgyr)
D = np.array(D)


# In[3]:


ax = plt.subplot(111)
ax.plot(Rgyr[:,0], Rgyr[:,1], 'r-', lw=2, label=r"$R_G$")
ax.set_xlabel("time (ps)")
ax.set_ylabel(r"radius of gyration $R_G$ ($\AA$)")
ax.figure.savefig("Rgyr.pdf")
plt.draw()


# In[4]:


ay = plt.subplot(111)
ay.plot(D[:,0], D[:,1], 'r-', lw=2, label=r"$R_D$")
ay.set_xlabel("time (ps)")
ay.set_ylabel(r"End to End distance ($\AA$)")
ay.figure.savefig("D.pdf")
plt.draw()


# In[12]:


ax = sns.distplot(Rgyr[:,1], vertical=True)
ax.set_xlabel("time (ps)")
ax.set_ylabel(r"radius of gyration $R_G$ ($\AA$)")


# In[13]:


import seaborn as sns, numpy as np
ay = sns.distplot(D[:,1], vertical=True)
ay.set_xlabel("time (ps)")
ay.set_ylabel(r"End to End distance ($\AA$)")


# In[ ]:

Python links

• Learn Python: https://pythonbasics.org/
• Python Tutorial: https://pythonprogramminglanguage.com