pyDEER
pyDEER is a python package for processing Double Electron-Electron Resonance (DEER) data.
The source code for pyDEER is available here.
The complete documentation for pyDEER is available here.
Installing pyDEER
python -m pip install pyDEERPython Requirements
- Python2 (>= 2.7)
- Python3 (>= 3.6)
Required Modules
- scipy
- numpy
python -m pip install scipy numpyImporting ELEXSYS Data
from matplotlib.pylab import *
import pyDEER as deer
# Define path to data
path = './data/20170602_NR119_test/DEER_NR119_55ave'
# Import data
t, data = deer.load_elexsys(path)
# Plot data
figure()
plot(t, data)
xlabel('Time (ns)')
ylabel('Signal (a.u.)')
show()Performing Tikhonov Regularization
import numpy as np
from matplotlib.pylab import *
import pyDEER as deer
# Define time and distance axes
t = np.r_[-100e-9:5e-6:500j]
r = np.r_[1.5e-9:10e-9:100j]
# Generate Kernel Matrix
K = deer.kernel(t, r)
# Simulate Gaussian P(r)
P_gauss = deer.gaussian(r, 0.2e-9, 4e-9)
# Calculate DEER trace from Gaussian P(r)
S = np.dot(K, P_gauss)
# Add noise to DEER trace
S_noisy = deer.add_noise(S, 0.1)
# Perform Tikhonov Regularization
P_lambda = deer.tikhonov(K, S_noisy, lambda_ = 1.0)
# Calculate Fit of DEER trace
S_fit = np.dot(K, P_lambda)
# Plot Result
figure()
plot(t*1e9, S_noisy, label = 'data')
plot(t*1e9, S_fit, label = 'Tikhonov')
xlabel('Time (ns)')
ylabel('Signal (a.u.)')
legend()
figure('P(r)')
plot(r*1e9, P_gauss, label = 'Exact')
plot(r*1e9, P_lambda, label = 'Tikhonov')
xlabel('r (nm)')
ylabel('P(r)')
legend()
show()
