Author: tlinnet
Date: Wed Sep 3 22:50:53 2014
New Revision: 25613
URL: http://svn.gna.org/viewcvs/relax?rev=25613&view=rev
Log:
Added initial systemtest for the protocol for repeated analysis of dispersion
data.
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=25613&r1=25612&r2=25613&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Wed Sep 3 22:50:53 2014
@@ -32,6 +32,7 @@
# relax module imports.
from auto_analyses import relax_disp
+from auto_analyses.relax_disp_repeat_cpmg import DIC_KEY_FORMAT,
Relax_disp_rep
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from lib.errors import RelaxError
@@ -5873,6 +5874,76 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2,
0.030959849811015544, 3)
+ def test_repeat_cpmg(self):
+ """Test the protocol for repeated dispersion analysis. The class:
relax_disp_repeat_cpmg.
+
+ U{task #7826<https://gna.org/task/index.php?7826>}. Write an python
class for the repeated analysis of dispersion data.
+ """
+
+ # Reset.
+ self.interpreter.reset()
+
+ # Define base path to files.
+ base_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'repeated_analysis'+sep+'SOD1'
+
+ # Setup dictionary with settings.
+ sdic = {}
+
+ # Define method to analyse for
+ method = 'FT'
+ sdic['method'] = method
+
+ # Spectrometer frqs in list.
+ sfrq_1 = 499.86214
+ sfrq_2 = 599.8908587
+ sfrqs = [sfrq_1, sfrq_2]
+
+ # Store in dictionary.
+ sdic['sfrqs'] = sfrqs
+
+ # Store unit for frq.
+ sdic['sfrq_unit'] = 'MHz'
+
+ # Store exp_type
+ sdic['exp_type'] = 'SQ CPMG'
+
+ # Initialize frq dics.
+ for frq in sfrqs:
+ key = DIC_KEY_FORMAT % (frq)
+ sdic[key] = {}
+
+ # Set keys.
+ e_1 = DIC_KEY_FORMAT % (sfrq_1)
+ e_2 = DIC_KEY_FORMAT % (sfrq_2)
+
+ # Store time T2.
+ sdic[e_1]['time_T2'] = 0.04
+ sdic[e_2]['time_T2'] = 0.06
+
+ # Set ncyc.
+ ncyc_1 = array([20, 0, 16, 10, 36, 2, 12, 4, 22, 18, 40, 14, 26, 8,
32, 24, 6, 28, 0])
+ ncyc_2 = array([28, 0, 4, 32, 60, 2, 10, 16, 8, 20, 52, 18, 40, 6,
12, 0, 24, 14, 22])
+
+ # Calculate the cpmg_frq and store.
+ sdic[e_1]['cpmg_frq'] = ncyc_1 / sdic[e_1]['time_T2']
+ sdic[e_2]['cpmg_frq'] = ncyc_2 / sdic[e_2]['time_T2']
+
+ # Define peak lists.
+ peaks_folder_1 = base_path +sep+ 'cpmg_disp_sod1d90a_060518' +sep+
'cpmg_disp_sod1d90a_060518_normal.fid' +sep+ 'analysis_FT' +sep+ 'ser_files'
+sep+ sdic['method']
+ peaks_folder_2 = base_path +sep+ 'cpmg_disp_sod1d90a_060521' +sep+
'cpmg_disp_sod1d90a_060521_normal.fid' +sep+ 'analysis_FT' +sep+ 'ser_files'
+sep+ sdic['method']
+ sdic[e_1]['peaks_folder'] = peaks_folder_1
+ sdic[e_2]['peaks_folder'] = peaks_folder_2
+
+ # Define folder to all rmsd files.
+ rmsd_folder_1 = base_path +sep+ 'cpmg_disp_sod1d90a_060518' +sep+
'cpmg_disp_sod1d90a_060518_normal.fid' +sep+ 'ft2_data'
+ rmsd_folder_2 = base_path +sep+ 'cpmg_disp_sod1d90a_060521' +sep+
'cpmg_disp_sod1d90a_060521_normal.fid' +sep+ 'ft2_data'
+ sdic[e_1]['rmsd_folder'] = rmsd_folder_1
+ sdic[e_2]['rmsd_folder'] = rmsd_folder_2
+
+ # Setup class with data.
+ RDR = Relax_disp_rep(sdic)
+
+
def test_r1rho_kjaergaard_auto(self):
"""Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho
relaxation dispersion experiments using the 'DPL' model.
r25613 - /trunk/test_suite/system_tests/relax_disp.py