Author: bugman
Date: Sat Nov 29 09:55:57 2014
New Revision: 26821
URL: http://svn.gna.org/viewcvs/relax?rev=26821&view=rev
Log:
Modified the relax_fit_saturation_recovery.py script to work as a system test.
This is the script from Andras Boeszoermenyi <Andras_Boeszoermenyi att hms
dott harvard dot edu>.
The change follows from the discussion of
http://thread.gmane.org/gmane.science.nmr.relax.devel/7308/focus=7369.
The status.install_path variable is now used to point to the location of the
files. The relax data
store ds.tmpdir variable is used for outputting all files. And commented out
user functions have
been deleted.
Modified:
trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
Modified:
trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py?rev=26821&r1=26820&r2=26821&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py
Sat Nov 29 09:55:57 2014
@@ -22,16 +22,26 @@
"""Script for relaxation curve fitting."""
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Missing temporary directory.
+if not hasattr(ds, 'tmpdir'):
+ ds.tmpdir = 'temp'
+
# Create the 'rx' data pipe.
pipe.create('rx', 'relax_fit')
-# Load the backbone amide 15N spins from a PDB file.
-#structure.read_pdb('Ap4Aase_new_3.pdb')
-#structure.load_spins(spin_id='@N')
+# The path to the data files.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'+sep+'saturation_recovery'
# Load the sequence.
-sequence.read(file='wr10_43_relax.seq', res_name_col=1, res_num_col=2,
spin_num_col=3, spin_name_col=4)
-spin.name(name='H')
+spin.create(spin_name='H', res_name='G', res_num=17)
spin.element(element='H')
spin.isotope(isotope='1H', spin_id='@H')
spin.name(name='HE1')
@@ -69,18 +79,12 @@
# Loop over the spectra.
for i in range(len(names)):
# Load the peak intensities (first the backbone NH, then the tryptophan
indole NH).
- spectrum.read_intensities(file=names[i]+'.list', spectrum_id=names[i],
int_method='height')
+ spectrum.read_intensities(file=names[i]+'.list', dir=data_path,
spectrum_id=names[i], int_method='height')
# Set the relaxation times.
relax_fit.relax_time(time=times[i], spectrum_id=names[i])
-# Specify the duplicated spectra.
-#spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
-#spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
-#spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
-#spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
-
-#maf# Spectrum baseplane noise for non-duplicated spectra
+# Spectrum baseplane noise for non-duplicated spectra
spectrum.baseplane_rmsd(error=92440.562999, spectrum_id='0.070s',
spin_id=None)
spectrum.baseplane_rmsd(error=91770.380636, spectrum_id='0.150s',
spin_id=None)
spectrum.baseplane_rmsd(error=95226.122047, spectrum_id='0.250s',
spin_id=None)
@@ -92,12 +96,8 @@
spectrum.baseplane_rmsd(error=95735.516944, spectrum_id='3.000s',
spin_id=None)
spectrum.baseplane_rmsd(error=106627.326030, spectrum_id='5.000s',
spin_id=None)
-
# Peak intensity error analysis.
spectrum.error_analysis()
-
-# Deselect unresolved spins.
-#deselect.read(file='unresolved', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5)
# Set the relaxation curve type.
relax_fit.select_model('exp')
@@ -116,17 +116,17 @@
monte_carlo.error_analysis()
# Save the relaxation rates.
-value.write(param='rx', file='rx.out', force=True)
+value.write(param='rx', file='rx.out', dir=ds.tmpdir, force=True)
# Save the results.
-results.write(file='results', force=True)
+results.write(file='results', dir=ds.tmpdir, force=True)
# Create Grace plots of the data.
-grace.write(y_data_type='chi2', file='chi2.agr', force=True) # Minimised
chi-squared value.
-grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial peak
intensity.
-grace.write(y_data_type='rx', file='rx.agr', force=True) # Relaxation
rate.
-grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
file='intensities.agr', force=True) # Average peak intensities.
-grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
norm=True, file='intensities_norm.agr', force=True) # Average peak
intensities (normalised).
+grace.write(y_data_type='chi2', file='chi2.agr', dir=ds.tmpdir, force=True)
# Minimised chi-squared value.
+grace.write(y_data_type='i0', file='i0.agr', dir=ds.tmpdir, force=True) #
Initial peak intensity.
+grace.write(y_data_type='rx', file='rx.agr', dir=ds.tmpdir, force=True) #
Relaxation rate.
+grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
file='intensities.agr', dir=ds.tmpdir, force=True) # Average peak
intensities.
+grace.write(x_data_type='relax_times', y_data_type='peak_intensity',
norm=True, file='intensities_norm.agr', dir=ds.tmpdir, force=True) #
Average peak intensities (normalised).
# Save the program state.
-state.save('rx.save', force=True)
+state.save('devnull', force=True)
r26821 - /trunk/test_suite/system_tests/scripts/relax_fit_saturation_recovery.py