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# We do not read the R1 data, but rather with R1.
# relax_data.read(ri_id='R1', ri_type='R1', frq=cdp.spectrometer_frq_list[0], file='R1_fitted_values.txt', dir=data_path, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
</source>
=== 2_pre_run_r2eff.py ===
This a script file to run the R2eff values only, with a high number of Monte Carlo simulations.
file: '''2_pre_run_r2eff.py'''.
<source lang="Python">
# Python module imports.
from os import getcwd, sep
import re
# relax module imports.
from auto_analyses.relax_disp import Relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
from specific_analyses.relax_disp.variables import MODEL_R2EFF
#########################################
#### Setup
# The data path
if not hasattr(ds, 'data_path'):
ds.data_path = getcwd()
# The models to analyse.
if not hasattr(ds, 'models'):
ds.models = [MODEL_R2EFF]
# The number of increments per parameter, to split up the search interval in grid search.
if not hasattr(ds, 'grid_inc'):
ds.grid_inc = 21
# The number of Monte-Carlo simulations, for the error analysis in the 'R2eff' model when exponential curves are fitted.
# For estimating the error of the fitted R2eff values,
# a high number should be provided. Later the high quality R2eff values will be read for subsequent model analyses.
if not hasattr(ds, 'exp_mc_sim_num'):
ds.exp_mc_sim_num = 10
# The result directory.
if not hasattr(ds, 'results_dir'):
ds.results_dir = getcwd() + sep + 'results_R2eff'
## The optimisation function tolerance.
## This is set to the standard value, and should not be changed.
#if not hasattr(ds, 'opt_func_tol'):
# ds.opt_func_tol = 1e-25
#Relax_disp.opt_func_tol = ds.opt_func_tol
#if not hasattr(ds, 'opt_max_iterations'):
# ds.opt_max_iterations = int(1e7)
#Relax_disp.opt_max_iterations = ds.opt_max_iteration
#########################################
### Run script with setup.
script(file='1_setup_r1rho.py', dir=ds.data_path)
# To speed up the analysis, only select a few spins.
deselect.all()
# Load the experiments settings file.
residues = open(ds.data_path+sep+'global_fit_residues.txt', 'r')
residueslines = residues.readlines()
residues.close()
# Split the line string into number and text.
r = re.compile("([a-zA-Z]+)([0-9]+)([a-zA-Z]+)(-)([a-zA-Z]+)")
for i, line in enumerate(residueslines):
if line[0] == "#":
continue
else:
re_split = r.match(line)
#print re_split.groups()
resn = re_split.group(1)
resi = int(re_split.group(2))
isotope = re_split.group(3)
select.spin(spin_id=':%i@%s'%(resi, isotope), change_all=False)
# Run the analysis.
Relax_disp(pipe_name=ds.pipe_name, pipe_bundle=ds.pipe_bundle, results_dir=ds.results_dir, models=ds.models, grid_inc=ds.grid_inc, exp_mc_sim_num=ds.exp_mc_sim_num)
</source>
= See also =
[[Category:Tutorials]]