Author: tlinnet
Date: Fri Aug 29 16:02:33 2014
New Revision: 25436
URL: http://svn.gna.org/viewcvs/relax?rev=25436&view=rev
Log:
Implemented systemtest: test_bug_negative_intensities_cpmg, to show lack of
error message to user.
Maybe these spins should be de-selected, or at least show a better warning.
task #7822(https://gna.org/task/index.php?7822): Implement user function to
estimate R2eff and associated errors for exponential curve fitting.
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/ncyc.txt
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/peaks_list_max_standard.ser
Modified:
trunk/test_suite/system_tests/relax_disp.py
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/ncyc.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/ncyc.txt?rev=25436&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/ncyc.txt
(added)
+++
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/ncyc.txt
Fri Aug 29 16:02:33 2014
@@ -0,0 +1,17 @@
+28 0.06 466.66666666666666666666 599.8908622 2.47e+03
+0 0.06 0 599.8908622 2.34e+03
+4 0.06 66.66666666666666666666 599.8908622 2.41e+03
+32 0.06 533.33333333333333333333 599.8908622 2.42e+03
+60 0.06 1000.00000000000000000000 599.8908622 2.45e+03
+2 0.06 33.33333333333333333333 599.8908622 2.42e+03
+10 0.06 166.66666666666666666666 599.8908622 2.42e+03
+16 0.06 266.66666666666666666666 599.8908622 2.44e+03
+8 0.06 133.33333333333333333333 599.8908622 2.39e+03
+20 0.06 333.33333333333333333333 599.8908622 2.4e+03
+50 0.06 833.33333333333333333333 599.8908622 2.42e+03
+18 0.06 300.00000000000000000000 599.8908622 2.46e+03
+40 0.06 666.66666666666666666666 599.8908622 2.41e+03
+6 0.06 100.00000000000000000000 599.8908622 2.45e+03
+12 0.06 200.00000000000000000000 599.8908622 2.45e+03
+0 0.06 0 599.8908622 2.39e+03
+24 0.06 400.00000000000000000000 599.8908622 2.45e+03
Added:
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/peaks_list_max_standard.ser
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/peaks_list_max_standard.ser?rev=25436&view=auto
==============================================================================
---
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/peaks_list_max_standard.ser
(added)
+++
trunk/test_suite/shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223/peaks_list_max_standard.ser
Fri Aug 29 16:02:33 2014
@@ -0,0 +1,17 @@
+REMARK SeriesTab Input: peaks_list.tab Output: peaks_list_max_standard.ser
+REMARK Mode: Maximum Dimensions: 2
+REMARK Input Region: X +/- 0 X-ZF: 1
+REMARK Analysis Region: X +/- 0
+REMARK Input Region: Y +/- 0 Y-ZF: 1
+REMARK Analysis Region: Y +/- 0
+
+VARS INDEX X_AXIS Y_AXIS X_PPM Y_PPM VOL ASS Z_A0 Z_A1 Z_A2 Z_A3 Z_A4 Z_A5
Z_A6 Z_A7 Z_A8 Z_A9 Z_A10 Z_A11 Z_A12 Z_A13 Z_A14 Z_A15 Z_A16
+FORMAT %5d %9.3f %9.3f %8.3f %8.3f %+e %s %7.4f %7.4f %7.4f %7.4f %7.4f
%7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f
+
+NULLVALUE -666
+NULLSTRING *
+
+ 1 1711.104 3040.110 8.514 121.681 +5.586445e+05 A3N-HN 1.0000
1.7492 0.9997 1.0075 1.0081 0.8991 1.0205 0.9893 1.0145 1.0078
1.0133 1.0020 0.9995 1.0020 1.0249 1.7571 1.0016
+ 2 2011.491 4112.494 8.025 117.805 +6.213668e+05 E4N-HN 1.0000
-1.6032 0.8322 0.9920 0.9951 0.8300 0.9458 0.9689 0.9246 0.9936
0.9914 0.9842 1.0011 0.8529 0.9727 1.5845 0.9822
+ 3 1974.019 2629.250 8.086 123.166 +4.592940e+05 F5N-HN 1.0000
1.8235 0.8614 1.0135 1.0134 0.8825 0.9332 0.9772 0.9273 0.9803
0.9986 1.0000 1.0012 0.8923 0.9421 1.8102 1.0062
+ 4 1608.518 3683.374 8.681 119.356 +5.293190e+05 D6N-HN 1.0000
1.6865 0.8531 1.0052 1.0065 0.8530 0.9280 0.9594 0.8989 0.9914
1.0115 0.9743 1.0063 0.8177 0.9264 1.6855 0.9981
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=25436&r1=25435&r2=25436&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Fri Aug 29 16:02:33 2014
@@ -1749,6 +1749,81 @@
# Auto-analysis execution.
with self.assertRaises(RelaxError):
relax_disp.Relax_disp(pipe_name='relax_disp',
results_dir=RESULTS_DIR, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL, insignificance=INSIGNIFICANCE, numeric_only=NUMERIC_ONLY)
+
+
+ def test_bug_negative_intensities_cpmg(self):
+ """Test data, where peak intensities are negative in CPMG
+
+ This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0509100103}. This is CPMG data with a fixed
relaxation time period. Experiment in 0.48 M GuHCl (guanidine hydrochloride).
+ """
+
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'KTeilum_FMPoulsen_MAkke_2006'+sep+'bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_041223'
+
+ # Create the spins
+
self.interpreter.spectrum.read_spins(file="peaks_list_max_standard.ser",
dir=data_path)
+
+ # Name the isotope for field strength scaling.
+ self.interpreter.spin.isotope(isotope='15N')
+
+ # Read the spectrum from NMRSeriesTab file. The "auto" will generate
spectrum name of form: Z_A{i}
+
self.interpreter.spectrum.read_intensities(file="peaks_list_max_standard.ser",
dir=data_path, spectrum_id='auto', int_method='height')
+
+ # Loop over the spectra settings.
+ ncycfile=open(data_path + sep + 'ncyc.txt', 'r')
+
+ # Make empty ncyclist
+ ncyclist = []
+
+ i = 0
+ for line in ncycfile:
+ ncyc = line.split()[0]
+ time_T2 = float(line.split()[1])
+ vcpmg = line.split()[2]
+ set_sfrq = float(line.split()[3])
+ rmsd_err = float(line.split()[4])
+
+ # Test if spectrum is a reference
+ if float(vcpmg) == 0.0:
+ vcpmg = None
+ else:
+ vcpmg = round(float(vcpmg), 3)
+
+ # Add ncyc to list
+ ncyclist.append(int(ncyc))
+
+ # Set the current spectrum id
+ current_id = "Z_A%s"%(i)
+
+ # Set the current experiment type.
+ self.interpreter.relax_disp.exp_type(spectrum_id=current_id,
exp_type='SQ CPMG')
+
+ # Set the peak intensity errors, as defined as the baseplane
RMSD.
+ self.interpreter.spectrum.baseplane_rmsd(error=rmsd_err,
spectrum_id=current_id)
+
+ # Set the NMR field strength of the spectrum.
+ self.interpreter.spectrometer.frequency(id=current_id,
frq=set_sfrq, units='MHz')
+
+ # Relaxation dispersion CPMG constant time delay T (in s).
+ self.interpreter.relax_disp.relax_time(spectrum_id=current_id,
time=time_T2)
+
+ # Set the relaxation dispersion CPMG frequencies.
+ self.interpreter.relax_disp.cpmg_setup(spectrum_id=current_id,
cpmg_frq=vcpmg)
+
+ i += 1
+
+ # Specify the duplicated spectra.
+ self.interpreter.spectrum.replicated(spectrum_ids=['Z_A1', 'Z_A15'])
+
+ # Delete replicate spectrum
+ #self.interpreter.spectrum.delete('Z_A15')
+
+ MODELS = ['R2eff']
+ GRID_INC = 5; MC_NUM = 3; MODSEL = 'AIC'
+
+ results_dir = ds.tmpdir
+
+ # Execute
+ relax_disp.Relax_disp(pipe_name='relax_disp',
results_dir=results_dir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM,
modsel=MODSEL)
def test_check_missing_r1(self):
r25436 - in /trunk/test_suite: shared_data/dispersion/KTeilum_FMPoulsen_MAkke_2006/bug_neg_int_acbp_cpmg_disp_048MGuHCl_40C_...