Author: bugman
Date: Fri Nov 29 11:24:22 2013
New Revision: 21712
URL: http://svn.gna.org/viewcvs/relax?rev=21712&view=rev
Log:
Synchronised the test_suite/shared_data/dispersion/Hansen/relax_disp.py with
the sample script.
This script now matches very closely with the
sample_scripts/relax_disp/cpmg_analysis.py sample
script. This is for sample script debugging purposes.
Modified:
trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py
Modified: trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py?rev=21712&r1=21711&r2=21712&view=diff
==============================================================================
--- trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py (original)
+++ trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py Fri Nov 29
11:24:22 2013
@@ -1,4 +1,30 @@
-# Script for CPMG relaxation dispersion curve fitting using Dr. Flemming
Hansen's data from http://dx.doi.org/10.1021/jp074793o.
+###############################################################################
+#
#
+# Copyright (C) 2013 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax (http://www.nmr-relax.com).
#
+#
#
+# This program is free software: you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation, either version 3 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# This program is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
+#
#
+###############################################################################
+
+"""Script for performing a full relaxation dispersion analysis using
CPMG-type data.
+
+This uses Dr. Flemming Hansen's data from
http://dx.doi.org/10.1021/jp074793o.
+
+This is here to test the ./sample_scripts/relax_disp/cpmg_analysis.py sample
script. The differences between the two files should be minimal.
+"""
# Python module imports.
from os import sep
@@ -21,8 +47,20 @@
# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
MC_NUM = 3
+# A flag which if True will activate Monte Carlo simulations for all models.
Note this will hugely increase the computation time.
+MC_SIM_ALL_MODELS = False
+
# The results directory.
RESULTS_DIR = 'temp'
+
+# The directory of results of an earlier analysis without clustering.
+PRE_RUN_DIR = None
+
+# The model selection technique to use.
+MODSEL = 'AIC'
+
+# The flag for only using numeric models in the final model selection.
+NUMERIC_ONLY = False
# The R2eff/R1rho value in rad/s by which to judge insignificance. If the
maximum difference between two points on all dispersion curves for a spin is
less than this value, that spin will be deselected.
INSIGNIFICANCE = 1.0
@@ -32,16 +70,16 @@
# Set up the data pipe.
#######################
+# The path to the data files.
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
+
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
-# The path to the data files.
-data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
-
# Load the sequence.
-sequence.read('fake_sequence.in', dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen',
res_num_col=1, res_name_col=2)
+sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1,
res_name_col=2)
# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling.
spin.name(name='N')
@@ -92,7 +130,7 @@
# Loop over the spectra.
for id, file, cpmg_frq, H_frq in data:
# Load the peak intensities.
- spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
+ spectrum.read_intensities(file=file, dir=DATA_PATH, spectrum_id=id,
int_method='height')
# Set the relaxation dispersion experiment type.
relax_disp.exp_type(spectrum_id=id, exp_type='SQ CPMG')
@@ -119,8 +157,8 @@
spectrum.error_analysis(subset=['800_reference.in', '800_66.667.in',
'800_133.33.in', '800_133.33.in.bis', '800_200.in', '800_266.67.in',
'800_333.33.in', '800_400.in', '800_466.67.in', '800_533.33.in',
'800_533.33.in.bis', '800_600.in', '800_666.67.in', '800_733.33.in',
'800_800.in', '800_866.67.in', '800_933.33.in', '800_933.33.in.bis',
'800_1000.in'])
# Deselect unresolved spins.
-deselect.read(file='unresolved', dir=data_path+sep+'500_MHz', res_num_col=1)
-deselect.read(file='unresolved', dir=data_path+sep+'800_MHz', res_num_col=1)
+deselect.read(file='unresolved', dir=DATA_PATH+sep+'500_MHz', res_num_col=1)
+deselect.read(file='unresolved', dir=DATA_PATH+sep+'800_MHz', res_num_col=1)
@@ -128,4 +166,4 @@
##########################
# Do not change!
-Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
insignificance=INSIGNIFICANCE)
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL, pre_run_dir=PRE_RUN_DIR, insignificance=INSIGNIFICANCE,
numeric_only=NUMERIC_ONLY, mc_sim_all_models=MC_SIM_ALL_MODELS)
r21712 - /trunk/test_suite/shared_data/dispersion/Hansen/relax_disp.py