def plot_tilted_landscape(LandscapeObj,min_landscape_kT=None,
fmt_f_label="{:.0f}",
max_landscape_kT=None,f_one_half_N=10e-12,**kwargs):
Obj = IWT_Util.TiltedLandscape(LandscapeObj,f_one_half_N=f_one_half_N,
**kwargs)
Obj.OffsetTilted_kT -= min(Obj.OffsetTilted_kT)
plt.plot(Obj.landscape_ext_nm,Obj.OffsetTilted_kT,color='b',alpha=0.7)
if (max_landscape_kT is None):
max_landscape_kT = max(Obj.OffsetTilted_kT)*1.5
if (min_landscape_kT is None):
min_landscape_kT = np.percentile(Obj.OffsetTilted_kT,5)-2
plt.ylim( min_landscape_kT,max_landscape_kT)
ylabel = ("Tilted (F=" + fmt_f_label + "pN) [kT]").format(f_one_half_N*1e12)
PlotUtilities.lazyLabel("Extension [nm]",ylabel,"",frameon=True)
return format_kcal_per_mol_second_axis_after_kT_axis()
def plot_free_landscape(LandscapeObj,**kwargs):
"""
plots a free landscape version extension
Args:
LandscapeObj: see plot_single_landscape
kwargs: passed to TiltedLandscape
Returns:
tilted landscape
"""
Obj = IWT_Util.TiltedLandscape(LandscapeObj,**kwargs)
plt.plot(Obj.landscape_ext_nm,Obj.Landscape_kT)
range = max(Obj.Landscape_kT) - min(Obj.Landscape_kT)
fudge = range/10
plt.ylim([-fudge,np.max(Obj.Landscape_kT)+fudge])
PlotUtilities.lazyLabel("","Landscape at F=0 [kT]","",frameon=True)
format_kcal_per_mol_second_axis_after_kT_axis()
return Obj
def run():
"""
<Description>
Args:
param1: This is the first param.
Returns:
This is a description of what is returned.
"""
# run a comparison of fwd,rev,both
base = "../Data/"
plot_both = dict(color='b', linestyle='--', label="Bi-directional")
plot_unfold = dict(color='m', linestyle=':', label="Only unfold")
plot_refold = dict(color='r', linestyle='-', label="Only refold")
input_files = [
[base + "UnfoldandRefold.pxp", "", plot_both],
[base + "JustUnfold.pxp", "-unfold_only 1", plot_unfold],
[base + "JustRefold.pxp", "-refold_only 1", plot_refold],
]
fig = PlotUtilities.figure(figsize=(3.5, 6))
f_one_half_N = 12e-12
for f, extra_str, plot_opt in input_files:
# run just the 'normal' IO
x_nm, G_kT, tilt = run_single(n_pairs=50,
v=50e-9,
f_one_half=f_one_half_N,
input_file=f,
extra_str=extra_str)
# save out the data
header = "# (C) PRH \n #Extension (nm),\t G (kT), \t G_tilt (kT)"
fname = f.split("/")[-1] + ".csv"
np.savetxt(X=np.array((x_nm, G_kT, tilt)).T,
fname=fname,
header=header,
delimiter=",")
ax1 = plt.subplot(2, 1, 1)
plt.plot(x_nm, G_kT, **plot_opt)
label_y = ("$G_0$ ($k_\mathrm{B}$T)")
PlotUtilities.lazyLabel("", label_y, "")
PlotUtilities.no_x_label(ax=ax1)
plt.subplot(2, 1, 2)
plt.plot(x_nm, tilt, **plot_opt)
label_y = ("$G_\mathrm{F_{1/2}=" + "{:.0f}".format(f_one_half_N*1e12) +\
"pN}$ ($k_\mathrm{B}$T)")
PlotUtilities.lazyLabel("x (nm)", label_y, "")
PlotUtilities.savefig(fig, "example_unfold_refold.png")
# run just the 'normal' IO
x_nm,G_kT,tilt = \
run_single(n_pairs=16,v=20e-9,input_file="../Data/input.pxp")
fig = PlotUtilities.figure()
plt.plot(x_nm, G_kT, 'r-')
PlotUtilities.lazyLabel("x (nm)", "$G_0$ ($k_\mathrm{B}$T)", "")
PlotUtilities.savefig(fig, "example_bidirectional.png")