Author: bugman
Date: Tue Oct 29 12:20:19 2013
New Revision: 21305
URL: http://svn.gna.org/viewcvs/relax?rev=21305&view=rev
Log:
Created the Relax_disp.test_hansen_cpmg_data_auto_analysis_r2eff system test.
This is to test the full dispersion auto-analysis on Flemming Hansen's CPMG
data using the original
R2eff data rather than the derived peak heights.
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py
- copied, changed from r21304,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
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=21305&r1=21304&r2=21305&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Tue Oct 29
12:20:19 2013
@@ -554,6 +554,84 @@
spin71 = return_spin(":71")
self.assertEqual(spin70.model, 'NS CPMG 2-site expanded')
self.assertEqual(spin71.model, 'No Rex')
+
+
+ def test_hansen_cpmg_data_auto_analysis_r2eff(self):
+ """Test of the dispersion auto-analysis using Dr. Flemming Hansen's
CPMG data (using the original R2eff data).
+
+ 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.
+ """
+
+ # Set the model.
+ ds.models = [
+ MODEL_NOREX,
+ MODEL_LM63,
+ MODEL_CR72,
+ MODEL_IT99
+ ]
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'hansen_r2eff_data.py')
+
+ # The 'No Rex' model checks.
+ self.interpreter.pipe.switch(pipe_name='No Rex')
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[0], 10.5340573632181, 4)
+ self.assertAlmostEqual(spin70.r2[1], 16.1113049920324, 4)
+ self.assertAlmostEqual(spin70.chi2, 2832.28562307, 4)
+ self.assertAlmostEqual(spin71.r2[0], 5.83137814994754, 4)
+ self.assertAlmostEqual(spin71.chi2, 73.6219146835821, 4)
+
+ # The 'LM63' model checks.
+ self.interpreter.pipe.switch(pipe_name='LM63')
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g" % ("phi_ex", spin70.phi_ex,
spin71.phi_ex))
+ print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[0], 6.7725779040626, 4)
+ self.assertAlmostEqual(spin70.r2[1], 6.6495102881274, 4)
+ self.assertAlmostEqual(spin70.phi_ex, 0.308228782539112, 4)
+ self.assertAlmostEqual(spin70.kex/10000, 4644.35027966526/10000, 4)
+ self.assertAlmostEqual(spin70.chi2, 137.64638621224, 4)
+ self.assertAlmostEqual(spin71.r2[0], 4.92986568906445, 4)
+ self.assertAlmostEqual(spin71.phi_ex, 0.0595701347673553, 4)
+ self.assertAlmostEqual(spin71.kex/10000, 2566.66176813506/10000, 4)
+ self.assertAlmostEqual(spin71.chi2, 2.31424715490254, 4)
+
+ # The 'CR72' model checks. These models have not reached the minima
due to the low quality optimisation!
+ self.interpreter.pipe.switch(pipe_name='CR72')
+ spin70 = return_spin(":70")
+ spin71 = return_spin(":71")
+ print("\n\nOptimised parameters:\n")
+ print("%-20s %-20s %-20s" % ("Parameter", "Value (:70)", "Value
(:71)"))
+ print("%-20s %20.15g %20.15g" % ("R2 (500 MHz)", spin70.r2[0],
spin71.r2[0]))
+ print("%-20s %20.15g %20.15g" % ("R2 (800 MHz)", spin70.r2[1],
spin71.r2[1]))
+ print("%-20s %20.15g %20.15g" % ("pA", spin70.pA, spin71.pA))
+ print("%-20s %20.15g %20.15g" % ("dw", spin70.dw, spin71.dw))
+ print("%-20s %20.15g %20.15g" % ("kex", spin70.kex, spin71.kex))
+ print("%-20s %20.15g %20.15g\n" % ("chi2", spin70.chi2, spin71.chi2))
+ self.assertAlmostEqual(spin70.r2[0], 6.97532271825192, 4)
+ self.assertAlmostEqual(spin70.r2[1], 9.45051817816538, 4)
+ self.assertAlmostEqual(spin70.pA, 0.989800346795472, 4)
+ self.assertAlmostEqual(spin70.dw, 5.61326926915313, 4)
+ self.assertAlmostEqual(spin70.kex/10000, 1713.02295468519/10000, 4)
+ self.assertAlmostEqual(spin70.chi2, 17.3955972313639, 4)
+ self.assertAlmostEqual(spin71.r2[0], 0.589453313816438, 2)
+ self.assertAlmostEqual(spin71.pA, 0.500005674625128, 2)
+ self.assertAlmostEqual(spin71.dw, 199.873875627265, 2)
+ self.assertAlmostEqual(spin71.kex, 10.7154862578618, 2)
+ self.assertAlmostEqual(spin71.chi2, 57.9468501661789, 2)
def test_hansen_cpmg_data_to_cr72(self):
Copied:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py
(from r21304,
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py?p2=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py&p1=branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py&r1=21304&r2=21305&rev=21305&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_data.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/hansen_r2eff_data.py
Tue Oct 29 12:20:19 2013
@@ -8,6 +8,9 @@
from data_store import Relax_data_store; ds = Relax_data_store()
from status import Status; status = Status()
+
+# Analysis variables.
+#####################
# The dispersion models.
MODELS = ['LM63']
@@ -30,6 +33,9 @@
+# Set up the data pipe.
+#######################
+
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
@@ -38,18 +44,63 @@
# The path to the data files.
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
-# Load the saved base pipe
-results.read(data_path+sep+'base_pipe')
-deselect.spin(":4")
+# 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)
-# Set the nuclear isotope data.
-spin.isotope('15N')
+# Name the spins so they can be matched to the assignments, and the isotope
for field strength scaling.
+spin.name(name='N')
+spin.isotope(isotope='15N')
-# Create the R2eff data pipe and load the results.
-pipe.create(pipe_name='R2eff', bundle=pipe_bundle, pipe_type='relax_disp')
-pipe.switch(pipe_name='R2eff')
-results.read(data_path+sep+'r2eff_pipe')
-deselect.spin(":4")
+# The spectral data - peak list file name, CPMG frequency (Hz), spectrometer
frequency in Hertz.
+data = [
+ ['500_MHz'+sep+'reference.in', None, 500e6],
+ ['500_MHz'+sep+'66.667.in', 66.6666, 500e6],
+ ['500_MHz'+sep+'133.33.in', 133.3333, 500e6],
+ ['500_MHz'+sep+'133.33.in.bis', 133.3333, 500e6],
+ ['500_MHz'+sep+'200.in', 200.0000, 500e6],
+ ['500_MHz'+sep+'266.67.in', 266.6666, 500e6],
+ ['500_MHz'+sep+'333.33.in', 333.3333, 500e6],
+ ['500_MHz'+sep+'400.in', 400.0000, 500e6],
+ ['500_MHz'+sep+'466.67.in', 466.6666, 500e6],
+ ['500_MHz'+sep+'533.33.in', 533.3333, 500e6],
+ ['500_MHz'+sep+'533.33.in.bis', 533.3333, 500e6],
+ ['500_MHz'+sep+'600.in', 600.0000, 500e6],
+ ['500_MHz'+sep+'666.67.in', 666.6666, 500e6],
+ ['500_MHz'+sep+'733.33.in', 733.3333, 500e6],
+ ['500_MHz'+sep+'800.in', 800.0000, 500e6],
+ ['500_MHz'+sep+'866.67.in', 866.6666, 500e6],
+ ['500_MHz'+sep+'933.33.in', 933.3333, 500e6],
+ ['500_MHz'+sep+'933.33.in.bis', 933.3333, 500e6],
+ ['500_MHz'+sep+'1000.in', 1000.0000, 500e6],
+ ['800_MHz'+sep+'reference.in', None, 800e6],
+ ['800_MHz'+sep+'66.667.in', 66.6666, 800e6],
+ ['800_MHz'+sep+'133.33.in', 133.3333, 800e6],
+ ['800_MHz'+sep+'133.33.in.bis', 133.3333, 800e6],
+ ['800_MHz'+sep+'200.in', 200.0000, 800e6],
+ ['800_MHz'+sep+'266.67.in', 266.6666, 800e6],
+ ['800_MHz'+sep+'333.33.in', 333.3333, 800e6],
+ ['800_MHz'+sep+'400.in', 400.0000, 800e6],
+ ['800_MHz'+sep+'466.67.in', 466.6666, 800e6],
+ ['800_MHz'+sep+'533.33.in', 533.3333, 800e6],
+ ['800_MHz'+sep+'533.33.in.bis', 533.3333, 800e6],
+ ['800_MHz'+sep+'600.in', 600.0000, 800e6],
+ ['800_MHz'+sep+'666.67.in', 666.6666, 800e6],
+ ['800_MHz'+sep+'733.33.in', 733.3333, 800e6],
+ ['800_MHz'+sep+'800.in', 800.0000, 800e6],
+ ['800_MHz'+sep+'866.67.in', 866.6666, 800e6],
+ ['800_MHz'+sep+'933.33.in', 933.3333, 800e6],
+ ['800_MHz'+sep+'933.33.in.bis', 933.3333, 800e6],
+ ['800_MHz'+sep+'1000.in', 1000.0000, 800e6]
+]
+
+# Loop over the spectra.
+for file, cpmg_frq, H_frq in data:
+ relax_disp.r2eff_read(file=file, dir=data_path, exp_type='CPMG',
frq=H_frq, disp_frq=cpmg_frq, res_num_col=1, data_col=2, error_col=3)
+
+# 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)
+
# Auto-analysis execution.
r21305 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/hansen_r2eff_data.py