def rd_analysis():
"""For scripting purposes this function should be reorganized.
Demonstrates workflow replaced by IPython Notebooks. Runs as main.
Returns
-------
Happy scientists
"""
curve_files = ['L25K_6p3_rd_600_full_heights.txt',
'L25K_6p3_rd_800_full_heights.txt']
endpt_files = ['l25k_6p3_600_rd_l9=2.txt','l25k_6p3_600_rd_l9=32.txt',
'l25k_6p3_800_rd_l9=2.txt','l25k_6p3_800_rd_l9=15.txt']
# Total R2 relaxation period (ms):
CT_B1 = 38.4
CT_B2 = 28.8
# Load data; 2 field strengths, 2 data types (full curves, endpoints):
# Full dispersion curve peak intensities:
B1curve, B2curve = [nmrfn.parse_rd(f) for f in curve_files]
B1curve['index']=B1curve.index # Eliminating triplicate measurement...
B1curve = B1curve.drop_duplicates(cols='index') #...
B1curve = B1curve.drop('index', axis=1) #...done.
# Curve endpoints peak intensities:
B1few, B1many, B2few, B2many = [nmrfn.parse_lt(f) for f in endpt_files]
# Compute Rex estimates from endpoints data
rexB1endpts = est_endpts(B1few, B1many, CT_B1)
rexB2endpts = est_endpts(B2few, B2many, CT_B2)
# Convert full dispersion curve peak intensities to R2 values
B1curveR2 = calc_R2series(B1curve, CT_B1)
B2curveR2 = calc_R2series(B2curve, CT_B2)
# Using highest-frequency CPMG R2 as intrinsic R2:
B1intR2 = B1curveR2.iloc[0,:]
B2intR2 = B2curveR2.iloc[0,:]
# Compute Rex estimates from fitting the full R2 curves:
kex0 = 1e3
Rex0 = 1.0
rexB1fit = fit_curves(B1curveR2, B1intR2, kex0, Rex0)
rexB2fit = fit_curves(B2curveR2, B2intR2, kex0, Rex0)
rex_output(rexB1fit, rexB2fit, rexB1endpts, rexB2endpts)
alpha_output(rexB1fit, rexB2fit, rexB1endpts, rexB2endpts)
plot_r2_cpmg(B1curveR2, 'R2_series_600_MHz')
plot_r2_cpmg(B2curveR2, 'R2_series_800_MHz')
print('ADDDATA\n', file = f)
# Function to print curve information and normalized peak intensity vs freq
def guardd_height(s, f):
text = \
'''INDEX\t{0}
ATOM\t{1}
RESIDUE\tpending
OBS\tVCPMG\tINTENSITY'''
print(text.format(s.name, args.atom), file = f)
norm = s.values[0]
for o, t in enumerate(s.index.values, start=1):
line = '{0}\t{1}\t{2}'
print(line.format(o, round(t,2), round(s.iloc[o-1]/norm,3)), file = f)
print('ADDDATA\n', file = f)
# Actual output procedure
out = open(args.fout, 'w')
guardd_dataset(args.name,args.ax,args.b0,args.temp,args.CT,args.coh,out)
heights = nmrfn.parse_rd(args.rh)
if args.outtype == 'r2':
r2_vals = calc_R2series(heights, args.CT)
for res in r2_vals:
guardd_r2(r2_vals[res], out)
if args.outtype == 'height':
for res in heights:
guardd_height(heights[res], out)
print('SEQUENCEFILE\t{0}'.format(args.seqlist), file = out)
out.close()
