matplotlib example hacky ramachandran (snippet)

Python matplotlib example 'hacky ramachandran'

Modules used in program:

import imp
import seaborn as sns
import numpy as np
import numpy.linalg
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 ramachandran

Python matplotlib example: hacky ramachandran


import argparse
import csv
import sys

import itertools
import MDAnalysis as mda

import matplotlib
matplotlib.use('Agg')  # noqa
%matplotlib inline
import matplotlib.pyplot as plt

import numpy as np
import numpy.linalg
from MDAnalysis.analysis.dihedrals import Ramachandran

import numpy.linalg
import numpy as np

import seaborn as sns


u = mda.Universe( "step3_charmm2omm.pdb","step5_1.dcd")

selection = "(segid %s )" % \
    ('PROF')


#if args.iresid1 is not None and args.iresid2 is not None:
#    selection = "(segid %s and resid %s-%s)" % \
#        (args.isegid1,args.iresid1,args.iresid2)

r = u.select_atoms(selection)

R = Ramachandran(r).run()
#print(R)
#print(dir(R))
#print(type(R))

fig, ax = plt.subplots(figsize=plt.figaspect(1))
R.plot(ax=ax,color='k', marker='.', ref=True)

a = R.angles.reshape(np.prod(R.angles.shape[:2]), 2)
plt.tight_layout()
#plt.savefig(args.o_plot1, format='png') # svg is better but sticking with png for now
plt.show()

sns.reset_defaults()
import imp
imp.reload(plt); imp.reload(sns)
with sns.axes_style("white"):
    #h = sns.jointplot(x=a[:,0],y=a[:,1], space=0)
    #h = sns.jointplot(x=a[:,0],y=a[:,1], kind="hex", space=0)
    h = sns.jointplot(x=a[:,0],y=a[:,1], kind="kde", space=0, n_levels=15)
    h.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)')
    h.ax_joint.set_xlim(-180, 180)
    h.ax_joint.set_ylim(-180, 180)

    #g = sns.JointGrid(x=a[:,0],y=a[:,1],space=0, xlim=(-180,180), ylim=(-180,180))
    #g = g.plot_joint(sns.kdeplot, shade=True ,cmap="Blues_d" )
    #g = g.plot_marginals(sns.kdeplot, shade=True)
    #g.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)')

    #k = (sns.jointplot(x=a[:,0],y=a[:,1],space=0,color="k").plot_joint(sns.kdeplot, zorder=0, n_levels=6))
    #k.set_axis_labels(r'$\Phi$ (degrees)', r'$\Psi$ (degrees)')
    #k.ax_joint.set_xlim(-181, 181)
    #k.ax_joint.set_ylim(-181, 181)


    #g.ax_joint.set_xlim(-180, 180)
    #g.ax_joint.set_ylim(-180, 180)
    plt.tight_layout()
    plt.show()
    #plt.savefig(args.o_plot2, format='png')

Python links

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