def plotpmf1D(xvst,xlabel="",ylabel="Free energy (k$_B$T)",bins=50,saveas=None,display=True,label=""):
"""Plot 1D pmf"""
if not display:
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
mid_bin,Fdata = pmfutil.pmf1D(xvst,bins=bins)
plt.plot(mid_bin,Fdata,lw=2,label=label)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
if saveas is not None:
plt.savefig(saveas)
if display:
plt.show()
def TS_probabilities(Tdirs,coordfile,contact_args):
""" Calculate the TS contact probabilities along some reaction coordinate
Parameters
----------
Tdirs : list
List of directory names to collect reaction coordinate file from
coordfile : str
Name of file containing reaction coordinate.
contact_args : object
Object containing the
"""
T = Tdirs[0].split("_")[0]
coordname = coordfile.split(".")[0]
if not os.path.exists("%s_profile/state_bounds.txt" % coordname):
# Determine state bounds from 1D profile
print "calculating state bounds"
coordvst = np.concatenate([np.loadtxt("%s/%s" % (x,coordfile)) for x in Tdirs ])
if not os.path.exists("%s_profile" % coordname):
os.mkdir("%s_profile" % coordname)
os.chdir("%s_profile" % coordname)
mid_bin, Fdata = pmfutil.pmf1D(coordvst,bins=40)
xinterp, F = pmfutil.interpolate_profile(mid_bin,Fdata)
minidx, maxidx = pmfutil.extrema_from_profile(xinterp,F)
min_bounds, max_bounds = pmfutil.state_bounds_from_profile(xinterp,F)
min_labels, max_labels = pmfutil.assign_state_labels(min_bounds,max_bounds)
pmfutil.save_state_bounds(T,min_bounds,max_bounds,min_labels,max_labels)
os.chdir("..")
with open("%s_profile/%s_state_bounds.txt" % (coordname,T),"r") as fin:
state_bins = np.array([ [float(x.split()[1]),float(x.split()[2])]
for x in fin.readlines() if x.split()[0].startswith("TS")])
else:
# Load state bounds
with open("%s_profile/state_bounds.txt" % coordname,"r") as fin:
state_bins = np.array([ [float(x.split()[1]),float(x.split()[2])]
for x in fin.readlines() if x.split()[0].startswith("TS")])
# Calculate the contact probability in TS
print "calculating TS"
contact_args.bins = state_bins
bin_edges, qi_vs_Q = simulation.calc.binned_contacts.calculate_binned_contacts_vs_q(contact_args)
TS = qi_vs_Q[0,:]
return TS
def plotpmf1D(xvst,
xlabel="",
ylabel="Free energy (k$_B$T)",
bins=50,
saveas=None,
display=True,
label=""):
"""Plot 1D pmf"""
if not display:
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
mid_bin, Fdata = pmfutil.pmf1D(xvst, bins=bins)
plt.plot(mid_bin, Fdata, lw=2, label=label)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
if saveas is not None:
plt.savefig(saveas)
if display:
plt.show()
parser.add_argument('--saveas', type=str, help='Optional. Filename to save plot.')
args = parser.parse_args()
filename = args.data
coord_name = filename.split(".")[0]
n_bins = args.n_bins
title = args.title
saveas = args.saveas
if filename.endswith("npy"):
coord = np.load(filename)
else:
coord = np.loadtxt(filename)
if filename == "Q.dat":
coord += np.random.normal(size=coord.shape[0])
mid_bin, Fdata = pmfutil.pmf1D(coord,bins=n_bins)
#xinterp, F = pmfutil.interpolate_profile(mid_bin,Fdata)
# Plot profile from data and interpolant
#plt.plot(xinterp,F(xinterp),lw=2,color='b',label="data")
plt.plot(mid_bin,Fdata,marker='o',color='b',label="fit")
plt.legend()
plt.xlabel("%s" % coord_name,fontsize=16)
plt.ylabel("F(%s) (k$_B$T)" % coord_name,fontsize=16)
plt.title(title)
if saveas is not None:
plt.savefig(saveas)
plt.show()
print T[i]
qtanh_files = [ "{}/{}".format(os.path.dirname(x),coordfile) for x in trajfiles[i] ]
qtanh_files_exist = [ os.path.exists(x) for x in qtanh_files ]
# this should work except I am experiencing a strange NaN error.
if np.all(qtanh_files_exist) and not recalculate:
qtanh = [ np.load(x) for x in qtanh_files ]
else:
qtanh = []
for n in range(len(trajfiles[i])):
traj = trajfiles[i][n]
qtanh_temp = np.array(qtanhsum_obs.map(md.load(traj, top=topfile)))
np.save(os.path.dirname(traj) + "/" + coordfile, qtanh_temp)
qtanh.append(qtanh_temp)
# calculate free energy profile and state definitions
mid_bin, Fdata = pmfutil.pmf1D(np.concatenate(qtanh), bins=40)
#plt.plot(mid_bin, Fdata, label=str(T[i]))
if not os.path.exists(coordname + "_profile"):
os.mkdir(coordname + "_profile")
os.chdir(coordname + "_profile")
np.savetxt("T_{}_mid_bin.dat".format(T[i]), mid_bin)
np.savetxt("T_{}_F.dat".format(T[i]), Fdata)
xinterp, F = pmfutil.interpolate_profile(mid_bin, Fdata)
minidx, maxidx = pmfutil.extrema_from_profile(xinterp, F)
F_fit = F(xinterp)
with open("T_{}_stab.dat".format(T[i]), "w") as fout:
fout.write(str(F_fit[minidx[1]] - F_fit[minidx[0]]))
help='Optional. Filename to save plot.')
args = parser.parse_args()
filename = args.data
coord_name = filename.split(".")[0]
n_bins = args.n_bins
title = args.title
saveas = args.saveas
if filename.endswith("npy"):
coord = np.load(filename)
else:
coord = np.loadtxt(filename)
if filename == "Q.dat":
coord += np.random.normal(size=coord.shape[0])
mid_bin, Fdata = pmfutil.pmf1D(coord, bins=n_bins)
#xinterp, F = pmfutil.interpolate_profile(mid_bin,Fdata)
# Plot profile from data and interpolant
#plt.plot(xinterp,F(xinterp),lw=2,color='b',label="data")
plt.plot(mid_bin, Fdata, marker='o', color='b', label="fit")
plt.legend()
plt.xlabel("%s" % coord_name, fontsize=16)
plt.ylabel("F(%s) (k$_B$T)" % coord_name, fontsize=16)
plt.title(title)
if saveas is not None:
plt.savefig(saveas)
plt.show()