Author: bugman
Date: Thu May 23 19:21:38 2013
New Revision: 19715
URL: http://svn.gna.org/viewcvs/relax?rev=19715&view=rev
Log:
Created the Relax_disp.test_hansen_cpmgfit_input system test.
This is for checking the operation of the relax_disp.cpmgfit_input user
function conversion of
Flemming Hansen's CPMG R2eff values into input files for CPMGFit. A relax
state file containing the
results of an analysis of an 'R2eff' model analysis of the truncated data has
been added to the test
suite data to speed up the test and to check the loading of dispersion state
files.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values.bz2
(with props)
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values.bz2?rev=19715&view=auto
==============================================================================
Binary file - no diff available.
Propchange:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values.bz2
------------------------------------------------------------------------------
svn:mime-type = application/octet-stream
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=19715&r1=19714&r2=19715&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu May 23
19:21:38 2013
@@ -80,6 +80,128 @@
# Execute the script.
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_data.py')
+
+
+ def test_hansen_cpmgfit_input(self):
+ """Conversion of Dr. Flemming Hansen's CPMG R2eff values into input
files for CPMGFit.
+
+ This uses the data from Dr. Flemming Hansen's paper at
http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed
relaxation time period.
+ """
+
+ # Load the state, preserving the temp directory.
+ tmpdir = ds.tmpdir
+ state = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'+sep+'r2eff_values'
+ self.interpreter.state.load(state, force=True)
+ ds.tmpdir = tmpdir
+
+ # Set up the model.
+ self.interpreter.relax_disp.select_model('LM63')
+
+ # Generate the input files.
+ self.interpreter.relax_disp.cpmgfit_input(force=True, dir=ds.tmpdir)
+
+ # What the files should contain.
+ batch_file = ['#! /bin/sh\n', '\n', 'cpmgfit -xmgr -f
spin_:70@xxxx\n', 'cpmgfit -xmgr -f spin_:71@xxxx\n']
+ spin1 = [
+ 'title :70@N\n',
+ 'fields 2 18.7892743865 11.7432964915\n',
+ 'function CPMG\n',
+ 'R2 1 10 20\n',
+ 'Rex 0 100.0 100\n',
+ 'tex 0 10.0 100\n',
+ 'xmgr\n',
+ '@ xaxis label "1/tcp (1/ms)"\n',
+ '@ yaxis label "R2(tcp) (rad/s)"\n',
+ '@ xaxis ticklabel format decimal\n',
+ '@ yaxis ticklabel format decimal\n',
+ '@ xaxis ticklabel char size 0.8\n',
+ '@ yaxis ticklabel char size 0.8\n',
+ '@ world xmin 0.0\n',
+ 'data\n',
+ '0.066667 16.045541 0.296491
11.743296 \n',
+ '0.133333 14.877925 0.234000
11.743296 \n',
+ '0.200000 14.357820 0.301228
11.743296 \n',
+ '0.266667 12.664495 0.299527
11.743296 \n',
+ '0.333333 12.363205 0.271194
11.743296 \n',
+ '0.400000 11.092532 0.285045
11.743296 \n',
+ '0.466667 10.566090 0.295090
11.743296 \n',
+ '0.533333 9.805807 0.235226
11.743296 \n',
+ '0.600000 9.564301 0.281865
11.743296 \n',
+ '0.666667 9.015634 0.275269
11.743296 \n',
+ '0.733333 8.607765 0.266371
11.743296 \n',
+ '0.800000 8.279997 0.274045
11.743296 \n',
+ '0.866667 8.474536 0.251836
11.743296 \n',
+ '0.933333 8.158973 0.220777
11.743296 \n',
+ '1.000000 7.988631 0.264123
11.743296 \n',
+ '0.066667 22.224914 0.157014
18.789274 \n',
+ '0.133333 21.230874 0.123960
18.789274 \n',
+ '0.200000 20.603704 0.162258
18.789274 \n',
+ '0.266667 20.327797 0.154694
18.789274 \n',
+ '0.333333 18.855377 0.159253
18.789274 \n',
+ '0.400000 18.537531 0.141982
18.789274 \n',
+ '0.466667 17.508069 0.139421
18.789274 \n',
+ '0.533333 16.035604 0.113450
18.789274 \n',
+ '0.600000 15.168192 0.145221
18.789274 \n',
+ '0.666667 14.431802 0.138125
18.789274 \n',
+ '0.733333 14.034137 0.131017
18.789274 \n',
+ '0.800000 12.920148 0.131678
18.789274 \n',
+ '0.866667 12.653673 0.139552
18.789274 \n',
+ '0.933333 12.610864 0.103480
18.789274 \n',
+ '1.000000 11.969303 0.135988
18.789274 \n'
+ ]
+ spin2 = [
+ 'title :71@N\n',
+ 'fields 2 18.7892743865 11.7432964915\n',
+ 'function CPMG\n',
+ 'R2 1 10 20\n',
+ 'Rex 0 100.0 100\n',
+ 'tex 0 10.0 100\n',
+ 'xmgr\n',
+ '@ xaxis label "1/tcp (1/ms)"\n',
+ '@ yaxis label "R2(tcp) (rad/s)"\n',
+ '@ xaxis ticklabel format decimal\n',
+ '@ yaxis ticklabel format decimal\n',
+ '@ xaxis ticklabel char size 0.8\n',
+ '@ yaxis ticklabel char size 0.8\n',
+ '@ world xmin 0.0\n',
+ 'data\n',
+ '0.066667 7.044342 0.174267
11.743296 \n',
+ '0.133333 6.781033 0.137976
11.743296 \n',
+ '0.200000 6.467623 0.171372
11.743296 \n',
+ '0.266667 6.333340 0.179931
11.743296 \n',
+ '0.333333 6.323238 0.162322
11.743296 \n',
+ '0.400000 6.005245 0.166673
11.743296 \n',
+ '0.466667 5.767052 0.168136
11.743296 \n',
+ '0.533333 5.476968 0.134411
11.743296 \n',
+ '0.600000 5.469949 0.157734
11.743296 \n',
+ '0.666667 5.295113 0.168230
11.743296 \n',
+ '0.733333 5.435648 0.163755
11.743296 \n',
+ '0.800000 5.410400 0.165309
11.743296 \n',
+ '0.866667 5.437554 0.158582
11.743296 \n',
+ '0.933333 5.176844 0.144974
11.743296 \n',
+ '1.000000 5.227232 0.162255
11.743296 \n'
+ ]
+
+ # Check the batch file.
+ file = open("%s%sbatch_run.sh" % (ds.tmpdir, sep))
+ lines = file.readlines()
+ file.close()
+ for i in range(len(lines)):
+ self.assertEqual(batch_file[i], lines[i])
+
+ # Check spin :70@N.
+ file = open("%s%sspin_%s.in" % (ds.tmpdir, sep, ':70@N'))
+ lines = file.readlines()
+ file.close()
+ for i in range(len(lines)):
+ self.assertEqual(spin1[i], lines[i])
+
+ # Check spin :71@N.
+ file = open("%s%sspin_%s.in" % (ds.tmpdir, sep, ':71@N'))
+ lines = file.readlines()
+ file.close()
+ for i in range(len(lines)):
+ self.assertEqual(spin2[i], lines[i])
def test_exp_fit(self):
r19715 - in /branches/relax_disp/test_suite: shared_data/dispersion/Hansen/r2eff_values.bz2 system_tests/relax_disp.py