Author: bugman
Date: Fri Nov 29 10:42:22 2013
New Revision: 21706
URL: http://svn.gna.org/viewcvs/relax?rev=21706&view=rev
Log:
Bug fixes for the non-functional R1rho_analysis.py relaxation dispersion
sample script.
This script was horribly broken, but it should now work. It can even be
executed from the base
relax directory or from within the sample_scripts/relax_disp/ directory and
perform the full
analysis (assuming write access to the relax source directory).
Modified:
trunk/sample_scripts/relax_disp/R1rho_analysis.py
Modified: trunk/sample_scripts/relax_disp/R1rho_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/relax_disp/R1rho_analysis.py?rev=21706&r1=21705&r2=21706&view=diff
==============================================================================
--- trunk/sample_scripts/relax_disp/R1rho_analysis.py (original)
+++ trunk/sample_scripts/relax_disp/R1rho_analysis.py Fri Nov 29 10:42:22 2013
@@ -58,16 +58,16 @@
# Set up the data pipe.
#######################
+# The path to the data files.
+DATA_PATH = '../../test_suite/shared_data/dispersion/r1rho_off_res_tp02'
+
# Create the data pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_disp'
pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
-# The path to the data files.
-data_path = 'r1rho_off_res_tp02'
-
# Load the sequence.
-sequence.read('fake_sequence.in', res_num_col=1, res_name_col=2)
+sequence.read('fake_sequence.in', dir=DATA_PATH, res_num_col=1,
res_name_col=2)
# Name the spins so they can be matched to the assignments.
spin.name(name='N')
@@ -77,37 +77,37 @@
# The spectral data - spectrum ID, peak list file name, spin-lock field
strength (Hz), the spin-lock offset (ppm), the relaxation time (s),
spectrometer frequency (Hz), and experimental error (RMSD of the base plane
noise for each spectrum).
data = [
- ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6,
200000.0]
- ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6,
200000.0]
- ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6,
200000.0]
- ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6,
200000.0]
- ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6,
200000.0]
- ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6,
200000.0]
+ ['ref_500MHz', 'ref_500MHz.list', None, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_1000.0_500MHz', 'nu_1000.0_500MHz.list', 1000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_1500.0_500MHz', 'nu_1500.0_500MHz.list', 1500.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_2000.0_500MHz', 'nu_2000.0_500MHz.list', 2000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_2500.0_500MHz', 'nu_2500.0_500MHz.list', 2500.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_3000.0_500MHz', 'nu_3000.0_500MHz.list', 3000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_3500.0_500MHz', 'nu_3500.0_500MHz.list', 3500.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_4000.0_500MHz', 'nu_4000.0_500MHz.list', 4000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_4500.0_500MHz', 'nu_4500.0_500MHz.list', 4500.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_5000.0_500MHz', 'nu_5000.0_500MHz.list', 5000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_5500.0_500MHz', 'nu_5500.0_500MHz.list', 5500.0, 110.0, 0.1, 500e6,
200000.0],
+ ['nu_6000.0_500MHz', 'nu_6000.0_500MHz.list', 6000.0, 110.0, 0.1, 500e6,
200000.0],
+ ['ref_800MHz', 'ref_800MHz.list', None, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_1000.0_800MHz', 'nu_1000.0_800MHz.list', 1000.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_1500.0_800MHz', 'nu_1500.0_800MHz.list', 1500.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_2000.0_800MHz', 'nu_2000.0_800MHz.list', 2000.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_2500.0_800MHz', 'nu_2500.0_800MHz.list', 2500.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_3000.0_800MHz', 'nu_3000.0_800MHz.list', 3000.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_3500.0_800MHz', 'nu_3500.0_800MHz.list', 3500.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_4000.0_800MHz', 'nu_4000.0_800MHz.list', 4000.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_4500.0_800MHz', 'nu_4500.0_800MHz.list', 4500.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_5000.0_800MHz', 'nu_5000.0_800MHz.list', 5000.0, 110.0, 0.1, 800e6,
200000.0],
+ ['nu_5500.0_800MHz', 'nu_5500.0_800MHz.list', 5500.0, 110.0, 0.1, 800e6,
200000.0],
['nu_6000.0_800MHz', 'nu_6000.0_800MHz.list', 6000.0, 110.0, 0.1, 800e6,
200000.0]
]
# Loop over the spectra.
for id, file, field, offset, relax_time, H_frq, rmsd in data:
# Load the peak intensities and set the errors.
- spectrum.read_intensities(file=file, dir=data_path, spectrum_id=id,
int_method='height')
- spectrum.baseplane_rmsd(spectrum_id=id, error=error)
+ spectrum.read_intensities(file=file, dir=DATA_PATH, spectrum_id=id,
int_method='height')
+ spectrum.baseplane_rmsd(spectrum_id=id, error=rmsd)
# Set the relaxation dispersion experiment type.
relax_disp.exp_type(spectrum_id=id, exp_type='R1rho')
@@ -125,18 +125,17 @@
spectrometer.frequency(id=id, frq=H_frq)
# Load the R1 data.
-relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6,
file='R1_500MHz.out', dir=data_path, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
-relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6,
file='R1_800MHz.out', dir=data_path, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6,
file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6,
file='R1_800MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
-# Clustering.
-relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
+# Clustering (only to be activated after an initial analysis without
clustering).
+#relax_disp.cluster(cluster_id='cluster', spin_id=':1-50')
# Read the chemical shift data.
-chemical_shift.read(file='ref_500MHz.list', dir=data_path)
+chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH)
# Deselect unresolved spins.
-deselect.read(file='unresolved', dir='500_MHz', res_num_col=1)
-deselect.read(file='unresolved', dir='800_MHz', res_num_col=1)
+deselect.read(file='unresolved', dir=DATA_PATH, res_num_col=1)
r21706 - /trunk/sample_scripts/relax_disp/R1rho_analysis.py