def plot_2D_Free_Energy(rc1, rc2, rc1n, rc2n, name, args, weights=None, temp=300, extra=None):
print "Starting the Plot"
nbins = args.bins
if args.method == "arb":
axis = None
elif args.method == "same":
axis = args.axis
##Plot a scatter plot
if not args.contour_only:
plt.figure()
plot_style = "scatter"
x, y, z = hist2d.make(rc1, rc2, nbins, nbins, temperature=temp, weight=weights, plot_style=plot_style, free_energy_plot=True, idx_smoothing=1)
cp = plt.scatter(x, y, s=10, c=z, marker='o', linewidth=0.)
if not extra == None:
plt.plot(extra[:,0], extra[:,1], "^k", markersize=6)
#vmax=7
if not axis == None:
plt.axis(axis)
plt.xlabel(rc1n, size=16)
plt.ylabel(rc2n, size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'Free Energy (kT units)',labelpad=pad)
plt.savefig("%s/%s_%s-%s-%s.png"%(args.save_dir, name, rc1n, rc2n, plot_style))
plt.close()
##Plot a contour plot
if not args.scatter_only:
ensure("%s/contour"%args.save_dir)
plt.figure()
plot_style = "contour"
xc, yc, zc = hist2d.make(rc1, rc2, nbins, nbins, temperature=temp, weight=weights, plot_style=plot_style, free_energy_plot=True, idx_smoothing=1)
cp = plt.contourf(xc, yc, zc, 20)
plt.contour(xc, yc, zc, cp.levels, colors='k', hold='on')
if not extra == None:
plt.plot(extra[:,0], extra[:,1], "^k", markersize=6)
if not axis == None:
plt.axis(axis)
plt.xlabel(rc1n, size=16)
plt.ylabel(rc2n, size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'Free Energy (kT units)',labelpad=pad)
plt.savefig("%s/contour/%s_%s-%s-%s.png"%(args.save_dir, name, rc1n, rc2n, plot_style))
plt.close()
def run():
parser = create_arg_parser()
args = parser.parse_args()
#read input files
x = []
for input_file in args.input_file_x:
file = reader.open(input_file)
vals = file.readlines()
# using readlines() of lsdmap reader, each row of x is a list
# corresponding to the coordinates of each config, thus
# needs to concatenate.
vals = np.concatenate(vals, axis=0)
x.append(vals)
x = np.hstack(np.array(x))
y = []
for input_file in args.input_file_y:
file = reader.open(input_file)
vals = file.readlines()
# using readlines() of lsdmap reader, each row of y is a list
# corresponding to the coordinates of each config, thus
# needs to concatenate.
vals = np.concatenate(vals, axis=0)
y.append(vals)
y = np.hstack(np.array(y))
if not args.nbins:
npoints = x.shape[0]
nbins = int(np.sqrt(npoints))
else:
nbins = args.nbins
if args.wfile is not None:
weight = []
for wfile in args.wfile:
file = reader.open(wfile)
vals = file.readlines()
weight.append(vals)
weight = np.hstack(np.array(weight))
else:
weight = None
plot_style = args.plot_style
free_energy_plot = args.free_energy_plot
idx_smoothing = args.idx_smoothing
x, y, z = hist2d.make(x, y, nbins, nbins, weight=weight, plot_style=plot_style, free_energy_plot=free_energy_plot, idx_smoothing=idx_smoothing)
if plot_style == 'scatter':
cp = plt.scatter(x, y, s=10, c=z, marker='o', linewidth=0., vmax=3.5)
elif plot_style == 'contour':
cp = plt.contourf(x, y, z)
plt.contour(x, y, z, cp.levels, colors='k', hold='on')
plt.xlabel(args.xlabel, size=16)
plt.ylabel(args.ylabel, size=16)
cb = plt.colorbar(cp)
pad = 10
if free_energy_plot is True:
cb.set_label(r'Free Energy (kcal/mol)',labelpad=pad)
else:
cb.set_label(r'Density', labelpad=pad)
plt.show()
subprocess.call("echo 0 | g_gyrate -xvg none -f " + gro_file + " -s " +
gro_file + " 1>/dev/null 2>&1",
shell=True)
tphi = np.loadtxt('rmsd.xvg')
tpsi = np.loadtxt('gyrate.xvg')
weight = np.loadtxt(w_file)
x = tphi[:, 1]
y = tpsi[:, 1]
nbins = 100
x, y, z = hist2d.make(x,
y,
nbins,
nbins,
plot_style='scatter',
weight=weight,
free_energy_plot=True,
idx_smoothing=3)
cp = plt.scatter(x, y, s=10, c=z, marker='o', linewidth=0.) #, vmax=3.5)
print "Free energy in range:", min(z), max(z)
plt.xlabel('RMSD (nm)', size=16)
plt.ylabel('Rg (nm)', size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'Free Energy (kcal/mol units)', labelpad=pad)
plt.axis([0.0, 1.0, 0.4, 1.4])
plt.savefig('plot_rgrmsd_iter' + str(i) + '.png', bbox_inches='tight')
dcs = np.loadtxt("results/iter" + str(i) + ".ev")
dcs = dcs[:, 0:3]
#prevent flipping
if max(dcs[:, 1]) < min(dcs[:, 1]) * -1:
dc1s = -dcs[:, 1]
else:
dc1s = dcs[:, 1]
if max(dcs[:, 2]) < min(dcs[:, 2]) * -1:
dc2s = -dcs[:, 2]
else:
dc2s = dcs[:, 2]
dc1s, dc2s, z = hist2d.make(dc1s,
dc2s,
100,
100,
plot_style='scatter',
free_energy_plot=True,
idx_smoothing=3)
cp = plt.scatter(dc1s, dc2s, s=10, c=z, marker='o', linewidth=0.)
plt.xlabel('DC1', size=16)
plt.ylabel('DC2', size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'population', labelpad=pad, size=16)
#cb.set_label(r'phi',labelpad=pad,size=16)
plt.savefig("plot_lsdmap_iter" + str(i) + '.png', bbox_inches='tight')
for i in c:
print i
plt.clf()
plt.xlabel('DC1', size=16)
plt.ylabel('DC2', size=16)
dcs = np.loadtxt("results/iter"+str(i)+".ev")
dcs = dcs[:,0:3]
#prevent flipping
if max(dcs[:,1])<min(dcs[:,1])*-1:
dc1s = -dcs[:,1]
else:
dc1s = dcs[:,1]
if max(dcs[:,2])<min(dcs[:,2])*-1:
dc2s = -dcs[:,2]
else:
dc2s = dcs[:,2]
dc1s, dc2s, z = hist2d.make(dc1s, dc2s, 100, 100, plot_style='scatter', free_energy_plot=True, idx_smoothing=3)
cp = plt.scatter(dc1s, dc2s, s=10, c=z, marker='o', linewidth=0.)
plt.xlabel('DC1', size=16)
plt.ylabel('DC2', size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'population',labelpad=pad,size=16)
#cb.set_label(r'phi',labelpad=pad,size=16)
plt.savefig("plot_lsdmap_iter"+str(i)+'.png', bbox_inches='tight')
c=np.append(a,b)
c=np.append(c,b2)
for i in c:
plt.clf()
w_file='results/iter'+str(i)+'.w'
gro_file='results/iter'+str(i)+'.gro'
subprocess.call("echo 0 0 | g_rms -xvg none -f " +gro_file+ " -s "+ref_file+".gro 1>/dev/null 2>&1", shell=True)
subprocess.call("echo 0 | g_gyrate -xvg none -f " +gro_file+ " -s " +gro_file+ " 1>/dev/null 2>&1", shell=True)
tphi = np.loadtxt('rmsd.xvg')
tpsi = np.loadtxt('gyrate.xvg')
weight = np.loadtxt(w_file)
x = tphi[:,1]
y = tpsi[:,1]
nbins = 100
x, y, z = hist2d.make(x, y, nbins, nbins, plot_style='scatter', weight=weight, free_energy_plot=True, idx_smoothing=3)
cp = plt.scatter(x, y, s=10, c=z, marker='o', linewidth=0.)#, vmax=3.5)
print "Free energy in range:", min(z), max(z)
plt.xlabel('RMSD (nm)', size=16)
plt.ylabel('Rg (nm)', size=16)
cb = plt.colorbar(cp)
pad = 10
cb.set_label(r'Free Energy (kcal/mol units)',labelpad=pad)
plt.axis([0.0,1.0, 0.4,1.4])
plt.savefig('plot_rgrmsd_iter'+str(i)+'.png', bbox_inches='tight')
