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plot.py
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plot.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# @File : plot.py
# @Date : 18-10-30
# @Author : luyang([email protected])
import os
import argparse
from matplotlib import ticker
import matplotlib.pyplot as plt
def parse_input():
parser = argparse.ArgumentParser(description='draw line charts')
parser.add_argument('-p', '--filepath', dest='filepath', required=True, help='path to protein-ligand pair folder')
args = parser.parse_args()
return args
def main():
args = parse_input()
filepath = args.filepath
# potential
potential_file = os.path.join(filepath,'analysis','potential.xvg')
with open(potential_file,'r') as f:
time = []
potential = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(int(float(cols[0])))
potential.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Energy Minimization")
ax.set_xlabel('Energy Minimization Step')
ax.set_ylabel('Potentail Energy$(kJ·mol^{-1})$')
ax.plot(time, potential, c='k', label='Potential')
formatter = ticker.ScalarFormatter(useMathText=True)
formatter.set_scientific(True)
formatter.set_powerlimits((-1, 1))
ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath,'analysis','potential.svg'))
# temperature
temperature_file = os.path.join(filepath, 'analysis', 'temperature.xvg')
with open(temperature_file, 'r') as f:
time = []
temperature = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(int(float(cols[0])))
temperature.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Temperature")
ax.set_xlabel('Time$(ps)$')
ax.set_ylabel('Temperature$(K)$')
ax.plot(time, temperature, c='k', label='Temperature')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'temperature.svg'))
# pressure
pressure_file = os.path.join(filepath, 'analysis', 'pressure.xvg')
with open(pressure_file, 'r') as f:
time = []
pressure = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(int(float(cols[0])))
pressure.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Pressure")
ax.set_xlabel('Time$(ps)$')
ax.set_ylabel('Pressure$(bar)$')
ax.plot(time, pressure, c='k', label='Pressure')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'pressure.svg'))
# density
density_file = os.path.join(filepath, 'analysis', 'density.xvg')
with open(density_file, 'r') as f:
time = []
density = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(int(float(cols[0])))
density.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Density")
ax.set_xlabel('Time$(ps)$')
ax.set_ylabel('Density$(kg·m^{-3})$')
ax.plot(time, density, c='k', label='Density')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'density.svg'))
# RMSD
rmsd_file = os.path.join(filepath, 'analysis', 'rmsd.xvg')
with open(rmsd_file, 'r') as f:
time = []
rmsd = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(float(cols[0]))
rmsd.append(float(cols[1]))
rmsd_xtal_file = os.path.join(filepath, 'analysis', 'rmsd_xtal.xvg')
with open(rmsd_xtal_file, 'r') as f:
time = []
rmsd_xtal = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(float(cols[0]))
rmsd_xtal.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("RMSD")
ax.set_xlabel('Time$(ns)$')
ax.set_ylabel('RMSD$(nm)$')
ax.plot(time, rmsd, c='k', label='Ref:Equilibrated')
ax.plot(time, rmsd_xtal, c='r', label='Ref:Crystal')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'rmsd.svg'))
# # gyrate
# gyrate_file = os.path.join(filepath, 'analysis', 'gyrate.xvg')
# with open(gyrate_file, 'r') as f:
# time = []
# gyrate = []
# for line in f.readlines():
# if line.startswith('#') or line.startswith('@'):
# continue
# else:
# cols = line.split()
# if len(cols) == 2:
# time.append(int(float(cols[0])))
# gyrate.append(float(cols[1]))
# fig = plt.figure()
# ax = fig.add_subplot(111)
# ax.set_title("Radius of gyration")
# ax.set_xlabel('Time$(ns)$')
# ax.set_ylabel('$R_{g}(nm)$')
# ax.plot(time, gyrate, c='k', label='')
# # formatter = ticker.ScalarFormatter(useMathText=True)
# # formatter.set_scientific(True)
# # formatter.set_powerlimits((-1, 1))
# # ax.yaxis.set_major_formatter(formatter)
# ax.legend()
# plt.savefig(os.path.join(filepath, 'analysis', 'gyrate.svg'))
# RMSF
rmsf_file = os.path.join(filepath, 'analysis', 'rmsf.xvg')
with open(rmsf_file, 'r') as f:
time = []
rmsf = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(float(cols[0]))
rmsf.append(float(cols[1]))
rmsf_xtal_file = os.path.join(filepath, 'analysis', 'rmsf_xtal.xvg')
with open(rmsf_xtal_file, 'r') as f:
time = []
rmsf_xtal = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 2:
time.append(float(cols[0]))
rmsf_xtal.append(float(cols[1]))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("RMSF")
ax.set_xlabel('Atom')
ax.set_ylabel('$RMSF(nm)$')
ax.plot(time, rmsf, c='k', label='Ref:Equilibrated')
ax.plot(time, rmsf_xtal, c='r', label='Ref:Crystal')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'rmsf.svg'))
# hbnum
hbnum_file = os.path.join(filepath, 'analysis', 'hbnum.xvg')
with open(hbnum_file, 'r') as f:
time = []
hbnum = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 3:
time.append(int(float(cols[0])))
hbnum.append(int(float(cols[1])))
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Hydrogen Bond Number")
ax.set_xlabel('Time$(ps)$')
ax.set_ylabel('Hydrogen bonds')
ax.scatter(time, hbnum, c='k', label='')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
# ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'hbnum.svg'))
# full_energy
full_energy_file = os.path.join(filepath, 'analysis', 'full_energy.dat')
with open(full_energy_file, 'r') as f:
time = []
E_VdW = []
E_Elec = []
E_Pol = []
E_Apol = []
E_Binding = []
for line in f.readlines():
if line.startswith('#') or line.startswith('@'):
continue
else:
cols = line.split()
if len(cols) == 17:
time.append(int(float(cols[0])))
E_VdW.append(float(cols[9])-float(cols[1])-float(cols[5]))
E_Elec.append(float(cols[10])-float(cols[2])-float(cols[6]))
E_Pol.append(float(cols[11]) - float(cols[3]) - float(cols[7]))
E_Apol.append(float(cols[12])-float(cols[4])-float(cols[8]))
E_Binding.append(E_VdW[-1]+ E_Elec[-1]+E_Pol[-1]+E_Apol[-1])
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("Energy")
ax.set_xlabel('Time$(ps)$')
ax.set_ylabel('Energy$(kJ·mol^{-1})$')
ax.plot(time, E_VdW, c='b', label='VdW')
ax.plot(time, E_Elec, c='g', label='Elec')
ax.plot(time, E_Pol, c='y', label='Pol')
ax.plot(time, E_Apol, c='k', label='Apol')
ax.plot(time, E_Binding, c='r', label='Binding')
# formatter = ticker.ScalarFormatter(useMathText=True)
# formatter.set_scientific(True)
# formatter.set_powerlimits((-1, 1))
# ax.yaxis.set_major_formatter(formatter)
ax.legend()
plt.savefig(os.path.join(filepath, 'analysis', 'full_energy.svg'))
if __name__ == "__main__":
main()