r5460 - /1.3/sample_scripts/relax_fit.py -- April 08, 2008 - 18:23

Author: bugman
Date: Tue Apr  8 18:23:30 2008
New Revision: 5460

URL: http://svn.gna.org/viewcvs/relax?rev=5460&view=rev
Log:
Updated the relax_fit.py sample script to the new design (no more run args).


Modified:
    1.3/sample_scripts/relax_fit.py

Modified: 1.3/sample_scripts/relax_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/relax_fit.py?rev=5460&r1=5459&r2=5460&view=diff
==============================================================================
--- 1.3/sample_scripts/relax_fit.py (original)
+++ 1.3/sample_scripts/relax_fit.py Tue Apr  8 18:23:30 2008
@@ -1,56 +1,55 @@
 # Script for relaxation curve fitting.
 
-# Create the run.
-name = 'rx'
-pipe.create(name, 'relax_fit')
+# Create the 'rx' data pipe.
+pipe.create('rx', 'relax_fit')
 
 # Load the backbone amide 15N spins from a PDB file.
 structure.read_pdb('Ap4Aase_new_3.pdb')
 structure.load_spins(spin_id='@N')
 
 # Load the peak intensities.
-relax_fit.read(name, file='T2_ncyc1.list', relax_time=0.0176)
-relax_fit.read(name, file='T2_ncyc1b.list', relax_time=0.0176)
-relax_fit.read(name, file='T2_ncyc2.list', relax_time=0.0352)
-relax_fit.read(name, file='T2_ncyc4.list', relax_time=0.0704)
-relax_fit.read(name, file='T2_ncyc4b.list', relax_time=0.0704)
-relax_fit.read(name, file='T2_ncyc6.list', relax_time=0.1056)
-relax_fit.read(name, file='T2_ncyc9.list', relax_time=0.1584)
-relax_fit.read(name, file='T2_ncyc9b.list', relax_time=0.1584)
-relax_fit.read(name, file='T2_ncyc11.list', relax_time=0.1936)
-relax_fit.read(name, file='T2_ncyc11b.list', relax_time=0.1936)
+relax_fit.read(file='T2_ncyc1.list', relax_time=0.0176)
+relax_fit.read(file='T2_ncyc1b.list', relax_time=0.0176)
+relax_fit.read(file='T2_ncyc2.list', relax_time=0.0352)
+relax_fit.read(file='T2_ncyc4.list', relax_time=0.0704)
+relax_fit.read(file='T2_ncyc4b.list', relax_time=0.0704)
+relax_fit.read(file='T2_ncyc6.list', relax_time=0.1056)
+relax_fit.read(file='T2_ncyc9.list', relax_time=0.1584)
+relax_fit.read(file='T2_ncyc9b.list', relax_time=0.1584)
+relax_fit.read(file='T2_ncyc11.list', relax_time=0.1936)
+relax_fit.read(file='T2_ncyc11b.list', relax_time=0.1936)
 
 # Calculate the peak intensity averages and the standard deviation of all 
spectra.
 relax_fit.mean_and_error(name)
 
 # Unselect unresolved residues.
-unselect.read(name, file='unresolved')
+unselect.read(file='unresolved')
 
 # Set the relaxation curve type.
-relax_fit.select_model(name, 'exp')
+relax_fit.select_model('exp')
 
 # Grid search.
-grid_search(name, inc=11)
+grid_search(inc=11)
 
 # Minimise.
-minimise('simplex', run=name, scaling=0, constraints=0)
+minimise('simplex', scaling=0, constraints=0)
 
 # Monte Carlo simulations.
-monte_carlo.setup(name, number=500)
+monte_carlo.setup(number=500)
 monte_carlo.create_data(name)
 monte_carlo.initial_values(name)
-minimise('simplex', run=name, scaling=0, constraints=0)
+minimise('simplex', scaling=0, constraints=0)
 monte_carlo.error_analysis(name)
 
 # Save the relaxation rates.
-value.write(name, param='rx', file='rx.out', force=1)
+value.write(param='rx', file='rx.out', force=1)
 
 # Create Grace plots of the data.
-grace.write(name, y_data_type='chi2', file='chi2.agr', force=1)    # 
Minimised chi-squared value.
-grace.write(name, y_data_type='i0', file='i0.agr', force=1)    # Initial 
peak intensity.
-grace.write(name, y_data_type='rx', file='rx.agr', force=1)    # Relaxation 
rate.
-grace.write(name, x_data_type='relax_times', y_data_type='ave_int', 
file='intensities.agr', force=1)    # Average peak intensities.
-grace.write(name, x_data_type='relax_times', y_data_type='ave_int', norm=1, 
file='intensities_norm.agr', force=1)    # Average peak intensities 
(normalised).
+grace.write(y_data_type='chi2', file='chi2.agr', force=1)    # Minimised 
chi-squared value.
+grace.write(y_data_type='i0', file='i0.agr', force=1)    # Initial peak 
intensity.
+grace.write(y_data_type='rx', file='rx.agr', force=1)    # Relaxation rate.
+grace.write(x_data_type='relax_times', y_data_type='ave_int', 
file='intensities.agr', force=1)    # Average peak intensities.
+grace.write(x_data_type='relax_times', y_data_type='ave_int', norm=1, 
file='intensities_norm.agr', force=1)    # Average peak intensities 
(normalised).
 
 # Display the Grace plots.
 grace.view(file='chi2.agr')