Author: tlinnet
Date: Tue Oct 7 18:43:52 2014
New Revision: 26196
URL: http://svn.gna.org/viewcvs/relax?rev=26196&view=rev
Log:
Added script to simulate dispersion profiles at different settings.
This shows that something is wrong.
The back-calculated values in the graphs are not equal to the interpolated
values.
There must be something wrong somewhere.
This list shows the chi2 values, and judging from the dispersion graphs, this
simply cannot be True.
10.405 2.414 6722.833
9.900 1.000 6722.159
9.900 2.333 6722.159
9.900 3.667 6722.159
9.900 5.000 6722.159
10.300 1.000 6722.156
10.300 2.333 6722.156
10.300 3.667 6722.156
10.300 5.000 6722.156
10.700 1.000 6726.040
10.700 2.333 6726.040
10.700 3.667 6726.040
10.700 5.000 6726.040
11.100 1.000 6732.256
11.100 2.333 6732.256
11.100 3.667 6732.256
11.100 5.000 6732.256
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_simulate_graphs.py
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_surface_chi2.txt
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_simulate_graphs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_simulate_graphs.py?rev=26196&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_simulate_graphs.py
(added)
+++
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_simulate_graphs.py
Tue Oct 7 18:43:52 2014
@@ -0,0 +1,149 @@
+# Python imports
+from os import getcwd, sep
+from numpy import array, float64, zeros
+
+# relax module imports.
+from lib.io import open_write_file, write_data
+from pipe_control.mol_res_spin import display_spin, generate_spin_string,
return_spin
+from pipe_control import value
+from specific_analyses.api import return_api
+
+# Create pipe
+pipe.create('relax_disp', 'relax_disp')
+
+# The specific analysis API object.
+api = return_api()
+
+# Variables
+prev_data_path = getcwd()
+result_filename = 'FT_-_TSMFK01_-_min_-_128_-_free_spins.bz2'
+
+# Read data in
+results.read(prev_data_path + sep + result_filename)
+
+# Get residue of interest. L61 is
+cur_spin_id = ":%i@%s"%(61, 'N')
+
+# Get the spin container.
+mol_name, cur_resi, cur_resn, cur_spin = return_spin(spin_id=cur_spin_id,
full_info=True)
+cur_spin_num = cur_spin.num
+cur_spin_name = cur_spin.name
+
+# Get the chi2 value
+pre_chi2 = cur_spin.chi2
+
+# Define surface map settings.
+dx_inc = 3
+
+# Lower bounds
+params = ['dw', 'k_AB']
+lower = [9.9, 1.0]
+upper = [11.1, 5.0]
+
+# Get the current point for clustered mininimisation.
+pcm = [cur_spin.dw, cur_spin.k_AB]
+print("Min cluster point %s=%3.3f, %s=%3.3f, with chi2=%3.3f" % (params[0],
pcm[0], params[1], pcm[1], pre_chi2))
+headings = [params[0], params[1], "chi2"]
+
+# Initialise.
+# Number of parameters
+n = 2
+
+# Get the default map bounds.
+bounds = zeros((n, 2), float64)
+
+# Lower bounds.
+bounds[:, 0] = array(lower, float64)
+
+# Upper bounds.
+bounds[:, 1] = array(upper, float64)
+
+# Setup the step sizes.
+step_size = zeros(n, float64)
+step_size = (bounds[:, 1] - bounds[:, 0]) / dx_inc
+
+# Placeholder to update values.
+values = zeros(n, float64)
+
+# Initial value of the first parameter.
+values[0] = bounds[0, 0]
+percent = 0.0
+percent_inc = 100.0 / (dx_inc + 1.0)**(n)
+print("%-10s%8.3f%-1s" % ("Progress:", percent, "%"))
+
+# Collect all chi2, to help finding a reasobale chi level.
+all_chi = []
+
+# Collect data.
+data = []
+# Append point as first data.
+data.append(["%3.3f"%pcm[0], "%3.3f"%pcm[1], "%3.3f"%pre_chi2 ])
+
+# Loop over the spin blocks.
+cluster_spin_ids = []
+for spin_ids in api.model_loop():
+ cluster_spin_ids.append(spin_ids)
+
+cur_spin_ids = cluster_spin_ids[0]
+
+# Display spins
+#display_spin()
+
+# Loop over the first parameter.
+# Start counter from 1003, so values correspond to line number.
+counter = 1003
+for i in range((dx_inc + 1)):
+ # Initial value of the second parameter.
+ values[1] = bounds[1, 0]
+
+ # Loop over the second parameter.
+ for j in range((dx_inc + 1)):
+ # Set the value.
+ value.set(val=values, param=params, spin_id=cur_spin_id, force=True)
+
+ # Calculate the function values.
+ api.calculate(spin_id=cur_spin_id, verbosity=0)
+
+ # Now copy the spin
+ new_res_name = "%s_%s=%1.1f_%s=%1.1f" % (cur_resn, params[0],
values[0], params[1], values[1])
+ #spin.create(spin_name=cur_spin_name, spin_num=cur_spin_num,
res_name=new_res_name, res_num=counter, mol_name=mol_name)
+ residue.create(res_num=counter, res_name=new_res_name,
mol_name=mol_name)
+ new_spin_id = ":%i@%s"%(counter, 'N')
+ spin.copy(pipe_from=None, spin_from=cur_spin_id, pipe_to=None,
spin_to=new_spin_id)
+
+ # Get the minimisation statistics for the model.
+ k_stat, n_stat, chi2 = api.model_statistics(spin_id=cur_spin_id)
+ #print(k_stat, n_stat, chi2, "point is %s=%3.3f, %s=%3.3f"%
(params[0], values[0], params[1], values[1]))
+
+ # Progress incrementation and printout.
+ percent = percent + percent_inc
+ print("%-10s%8.3f%-8s%-8g" % ("Progress:", percent, "%, " +
repr(values) + ", f(x): ", chi2))
+
+ # Append to data.
+ data.append(["%3.3f"%values[0], "%3.3f"%values[1], "%3.3f"%chi2 ])
+
+ # Save all values of chi2. To help find reasonale level for the
Innermost, Inner, Middle and Outer Isosurface.
+ all_chi.append(chi2)
+
+ # Increment the value of the second parameter.
+ values[1] = values[1] + step_size[1]
+
+ counter += 1
+
+ # Increment the value of the first parameter.
+ values[0] = values[0] + step_size[0]
+
+print("\nMin cluster point %s=%3.3f, %s=%3.3f, with chi2=%3.3f" %
(params[0], pcm[0], params[1], pcm[1], pre_chi2))
+
+# Open file
+file_name = '3_surface_chi2.txt'
+surface_file = open_write_file(file_name=file_name, dir=None, force=True)
+write_data(out=surface_file, headings=headings, data=data)
+
+# Close file
+surface_file.close()
+
+# Check spins.
+display_spin()
+
+relax_disp.plot_disp_curves(dir='grace', y_axis='r2_eff', x_axis='disp',
num_points=1000, extend_hz=500.0, extend_ppm=500.0, interpolate='disp',
force=False)
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_surface_chi2.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_surface_chi2.txt?rev=26196&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_surface_chi2.txt
(added)
+++
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/3_surface_chi2.txt
Tue Oct 7 18:43:52 2014
@@ -0,0 +1,18 @@
+# dw k_AB chi2
+10.405 2.414 6722.833
+9.900 1.000 6722.159
+9.900 2.333 6722.159
+9.900 3.667 6722.159
+9.900 5.000 6722.159
+10.300 1.000 6722.156
+10.300 2.333 6722.156
+10.300 3.667 6722.156
+10.300 5.000 6722.156
+10.700 1.000 6726.040
+10.700 2.333 6726.040
+10.700 3.667 6726.040
+10.700 5.000 6726.040
+11.100 1.000 6732.256
+11.100 2.333 6732.256
+11.100 3.667 6732.256
+11.100 5.000 6732.256
r26196 - /trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/surface_chi2_clustered_fitting/