Author: tlinnet
Date: Mon Sep 8 18:49:47 2014
New Revision: 25689
URL: http://svn.gna.org/viewcvs/relax?rev=25689&view=rev
Log:
Modified system test to follow the new functions in the auto analysis.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25689&r1=25688&r2=25689&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Sep 8 18:49:47 2014
@@ -38,8 +38,9 @@
from lib.errors import RelaxError
from lib.io import extract_data, get_file_path
from lib.spectrum.nmrpipe import show_apod_extract, show_apod_rmsd,
show_apod_rmsd_dir_to_files, show_apod_rmsd_to_file
-from pipe_control.mol_res_spin import generate_spin_string, return_spin,
spin_loop
+from pipe_control.mol_res_spin import display_spin, generate_spin_string,
return_spin, spin_loop
from pipe_control.minimise import assemble_scaling_matrix
+from pipe_control.pipes import display
from specific_analyses.relax_disp.checks import check_missing_r1
from specific_analyses.relax_disp.estimate_r2eff import estimate_r2eff
from specific_analyses.relax_disp.data import average_intensity,
check_intensity_errors, generate_r20_key, get_curve_type,
has_exponential_exp_type, has_r1rho_exp_type, loop_exp_frq,
loop_exp_frq_offset_point, loop_exp_frq_offset_point_time, loop_time,
return_grace_file_name_ini, return_param_key_from_data, spin_ids_to_containers
@@ -5950,7 +5951,7 @@
sdic[e_2]['rmsd_folder'] = rmsd_folder_2
# Define temporary folder.
- #sdic['results_dir'] = self.tmpdir
+ sdic['results_dir'] = self.tmpdir
# Setup class with data.
RDR = Relax_disp_rep(sdic)
@@ -5958,41 +5959,66 @@
# Setup base information.
RDR.set_base_cpmg(glob_ini=128)
+ #methods = ['FT', 'MDD']
+ methods = ['FT']
+
# Set the intensity.
- #RDR.set_int(list_glob_ini=[128, 126])
-
- # Now calculate R2eff.
- RDR.calc_r2eff(list_glob_ini=[128, 126, 6])
-
- # Minimise.
- #RDR.minimise_model(model=MODEL_CR72, list_glob_ini=[128, 126])
-
- # Try for bad data.
- #RDR.calc_r2eff(list_glob_ini=[6, 4])
-
- # Change method.
- RDR.set_self(key='method', value='MDD')
-
- # Now calculate R2eff.
- RDR.calc_r2eff(list_glob_ini=[128, 126])
-
- # Minimise.
- #RDR.minimise_model(model=MODEL_CR72, list_glob_ini=[128, 126])
-
- # Collect r2eff values.
- r2eff_ft = RDR.col_r2eff(method='FT', list_glob_ini=[128, 126, 6])
-
- # Collect r2eff values.
- r2eff_mdd = RDR.col_r2eff(method='MDD', list_glob_ini=[128, 126])
-
- # Get R2eff stats.
- r2eff_stat_dic = RDR.get_r2eff_stat_dic(list_r2eff_dics=[r2eff_ft,
r2eff_mdd], list_glob_ini=[128, 126, 6])
-
- # Plot R2eff stats
- RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic, methods=['FT'],
list_glob_ini=[128, 126, 6], show=True)
+ #RDR.set_int(methods=methods, list_glob_ini=[128, 126])
+
+ if True:
+ # Now calculate R2eff.
+ RDR.calc_r2eff(methods=methods, list_glob_ini=[128, 126])
+
+ # Try for bad data.
+ #RDR.calc_r2eff(methods=['FT'], list_glob_ini=[6, 4])
+
+ if False:
+ # Collect r2eff values.
+ r2eff_ft = RDR.col_r2eff(method='FT', list_glob_ini=[128,
126, 6])
+
+ # Collect r2eff values.
+ r2eff_mdd = RDR.col_r2eff(method='MDD', list_glob_ini=[128,
126])
+
+ # Get R2eff stats.
+ r2eff_stat_dic =
RDR.get_r2eff_stat_dic(list_r2eff_dics=[r2eff_ft, r2eff_mdd],
list_glob_ini=[128, 126, 6])
+
+ # Plot R2eff stats
+ RDR.plot_r2eff_stat(r2eff_stat_dic=r2eff_stat_dic,
methods=['FT'], list_glob_ini=[128, 126, 6], show=True)
+
+ # Do minimisation
+ if True:
+ # Deselect all spins.
+ #self.interpreter.spin.display()
+ RDR.deselect_all(methods=methods, model='setup',
model_from=MODEL_R2EFF, analysis='grid setup', analysis_from='int',
list_glob_ini=[128, 126])
+ #self.interpreter.spin.display()
+
+ # Select spins.
+ RDR.select_spin(spin_id=':2,3', methods=methods, model='setup',
analysis='grid setup', list_glob_ini=[128, 126])
+ #self.interpreter.spin.display()
+
+ # Set R20 from min R2eff in preparation for Grid search.
+ RDR.r20_from_min_r2eff(methods=methods, model=MODEL_CR72,
model_from='setup', analysis='grid setup', list_glob_ini=[128, 126])
+
+ # Set kex for Grid search.
+ RDR.value_set(methods=methods, val=1000., param='kex',
model=MODEL_CR72, analysis='grid setup', list_glob_ini=[128, 126], force=True)
+ # Get pipe and print.
+ #test_pipe_name = RDR.name_pipe(method='FT', model=MODEL_CR72,
analysis='grid setup', glob_ini='128')
+ #RDR.spin_display_params(pipe_name=test_pipe_name)
+
+ # Do Grid search.
+ RDR.minimise_grid_search(inc=11, methods=methods,
model=MODEL_CR72, analysis='grid', analysis_from='grid setup',
list_glob_ini=[128, 126])
+ # Get pipe and print.
+ test_pipe_name = RDR.name_pipe(method='FT', model=MODEL_CR72,
analysis='grid', glob_ini='128')
+ RDR.spin_display_params(pipe_name=test_pipe_name)
+
+ # Minimise
+ RDR.minimise_execute(methods=methods, model=MODEL_CR72,
analysis='min', analysis_from='grid', list_glob_ini=[128, 126])
+ # Get pipe and print.
+ test_pipe_name = RDR.name_pipe(method='FT', model=MODEL_CR72,
analysis='min', glob_ini='128')
+ RDR.spin_display_params(pipe_name=test_pipe_name)
# Print the pipes.
- self.interpreter.pipe.display()
+ display(sort=True, rev=True)
def test_r1rho_kjaergaard_auto(self):
r25689 - /trunk/test_suite/system_tests/relax_disp.py