Author: tlinnet
Date: Fri May 2 13:14:17 2014
New Revision: 22924
URL: http://svn.gna.org/viewcvs/relax?rev=22924&view=rev
Log:
Removed trailing spaces in file for Relax_disp systemtests.
Modified:
trunk/test_suite/system_tests/relax_disp.py
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=22924&r1=22923&r2=22924&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Fri May 2 13:14:17 2014
@@ -62,7 +62,7 @@
"test_value_write_calc_rotating_frame_params_auto_analysis"
]
- # Store in the status object.
+ # Store in the status object.
if methodName in to_skip:
status.skipped_tests.append([methodName, 'Relax
curve-fitting C module', self._skip_type])
@@ -245,7 +245,7 @@
def setup_sod1wt_t25(self, pipe_name, pipe_type, pipe_name_r2eff,
select_spin_index):
"""Setup of data SOD1-WT CPMG. From paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}.
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
'SOD1-WT' CPMG data to the CR72 dispersion model.
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
@@ -282,25 +282,25 @@
ncyc = ncycs[i]
vcpmg = ncyc/time_T2
- # Test if spectrum is a reference
- if float(vcpmg) == 0.0:
- vcpmg = None
- else:
+ # Test if spectrum is a reference
+ if float(vcpmg) == 0.0:
+ vcpmg = None
+ else:
vcpmg = round(float(vcpmg),3)
# Set current id
current_id = id_list[i]
- # Set the current experiment type.
+ # Set the current experiment type.
self.interpreter.relax_disp.exp_type(spectrum_id=current_id,
exp_type='SQ CPMG')
- # Set the NMR field strength of the spectrum.
+ # Set the NMR field strength of the spectrum.
self.interpreter.spectrometer.frequency(id=current_id,
frq=sfrq, units='Hz')
- # Relaxation dispersion CPMG constant time delay T (in s).
+ # 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.
+ # Set the relaxation dispersion CPMG frequencies.
self.interpreter.relax_disp.cpmg_frq(spectrum_id=current_id,
cpmg_frq=vcpmg)
# Define replicated
@@ -317,11 +317,11 @@
#############
# Define the 64 residues which was used for Global fitting
- glob_assn = ["G10N-H", "D11N-H", "Q15N-H", "G16N-H", "G37N-H",
"G41N-H", "L42N-H", "H43N-H", "H46N-H", "V47N-H", "E49N-H",
- "E50N-H", "E51N-H", "N53N-H", "T54N-H", "G56N-H", "C57N-H",
"T58N-H", "G61N-H", "H63aN-H", "F64aN-H", "N65aN-H",
- "L67N-H", "S68N-H", "K70N-H", "G72N-H", "G73N-H", "K75N-H",
"E78N-H", "R79N-H", "H80N-H", "V81N-H", "G82N-H",
- "G85N-H", "N86N-H", "V87N-H", "S102N-H", "V103N-H", "I104N-H",
"S105N-H", "A111N-H", "I112N-H", "R115N-H",
- "V118N-H", "E121N-H", "A123N-H", "L126N-H", "G127N-H", "K128N-H",
"G129N-H", "G130N-H", "N131N-H", "E133N-H",
+ glob_assn = ["G10N-H", "D11N-H", "Q15N-H", "G16N-H", "G37N-H",
"G41N-H", "L42N-H", "H43N-H", "H46N-H", "V47N-H", "E49N-H",
+ "E50N-H", "E51N-H", "N53N-H", "T54N-H", "G56N-H", "C57N-H",
"T58N-H", "G61N-H", "H63aN-H", "F64aN-H", "N65aN-H",
+ "L67N-H", "S68N-H", "K70N-H", "G72N-H", "G73N-H", "K75N-H",
"E78N-H", "R79N-H", "H80N-H", "V81N-H", "G82N-H",
+ "G85N-H", "N86N-H", "V87N-H", "S102N-H", "V103N-H", "I104N-H",
"S105N-H", "A111N-H", "I112N-H", "R115N-H",
+ "V118N-H", "E121N-H", "A123N-H", "L126N-H", "G127N-H", "K128N-H",
"G129N-H", "G130N-H", "N131N-H", "E133N-H",
"S134N-H", "T135N-H", "T137N-H", "G138N-H", "N139N-H", "A140N-H",
"G141N-H", "S142N-H", "R143N-H", "C146N-H", "G147N-H"]
# Test number of global
@@ -347,7 +347,7 @@
############# Deselect all spins, and select few spins
## Deselect all spins, and select a few for analysis
- self.interpreter.deselect.all()
+ self.interpreter.deselect.all()
# Select few spins
for i in select_spin_index:
@@ -356,8 +356,8 @@
##############
# Prepare for R2eff calculation
- self.interpreter.pipe.copy(pipe_from=pipe_name,
pipe_to=pipe_name_r2eff)
- self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff)
+ self.interpreter.pipe.copy(pipe_from=pipe_name,
pipe_to=pipe_name_r2eff)
+ self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff)
# Select model for points calculation
MODEL = "R2eff"
@@ -402,7 +402,7 @@
# Total time of CPMG block.
Trelax=0.04
- # First set the
+ # First set the
for i in range(len(ids)):
id = ids[i]
# Set the spectrometer frequency.
@@ -420,11 +420,11 @@
self.interpreter.relax_disp.cpmg_frq(spectrum_id=id,
cpmg_frq=nu_cpmg)
# Prepare for R2eff reading.
- self.interpreter.pipe.copy(pipe_from=pipe_name,
pipe_to=pipe_name_r2eff)
+ self.interpreter.pipe.copy(pipe_from=pipe_name,
pipe_to=pipe_name_r2eff)
self.interpreter.pipe.switch(pipe_name=pipe_name_r2eff)
# Try reading the R2eff file.
- self.interpreter.relax_disp.r2eff_read_spin(id="CPMG",
file="test_w_error.out", dir=data_path, spin_id=':1@N', disp_point_col=1,
data_col=2, error_col=3)
+ self.interpreter.relax_disp.r2eff_read_spin(id="CPMG",
file="test_w_error.out", dir=data_path, spin_id=':1@N', disp_point_col=1,
data_col=2, error_col=3)
# Check the global data.
data = [
@@ -475,8 +475,8 @@
# Change pipe.
pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL)
- self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
- self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
+ self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
+ self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
# Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
@@ -538,7 +538,7 @@
dw_ppm=2.
#relaxation rate of ground (s-1)
R2g=2.
- #relaxation rate of excited (s-1)
+ #relaxation rate of excited (s-1)
R2e=100.
#self.assertEqual(cdp.mol[0].res[0].spin[0].kex, kex)
@@ -2561,7 +2561,7 @@
Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
- - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
+ - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
- 0.483 0.89623903 2.4503699912708878
- 0.545 1.1694838
- 0.545 1.1761503
@@ -2627,7 +2627,7 @@
Figure 3 shows the ln( k_a [s^-1]) for different concentrations of
GuHCl. The precise values are:
- - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
+ - [GuHCL][M] ln(k_a[s^-1]) k_a[s^-1]
- 0.483 0.89623903 2.4503699912708878
- 0.545 1.1694838
- 0.545 1.1761503
@@ -2901,9 +2901,9 @@
self.interpreter.chemical_shift.read(file='1_0_46_0_max_standard.ser',
dir=data_path+sep+'peak_lists')
# Test the chemical shift data.
- cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999,
122.610, 118.602, 118.291, 115.393,
- 121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748,
118.103, 119.421, 119.317, 119.386, 117.279,
- 122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318,
117.770, 119.948, 119.759, 118.314, 118.160,
+ cs = [122.223, 122.162, 114.250, 125.852, 118.626, 117.449, 119.999,
122.610, 118.602, 118.291, 115.393,
+ 121.288, 117.448, 116.378, 116.316, 117.263, 122.211, 118.748,
118.103, 119.421, 119.317, 119.386, 117.279,
+ 122.103, 120.038, 116.698, 111.811, 118.639, 118.285, 121.318,
117.770, 119.948, 119.759, 118.314, 118.160,
121.442, 118.714, 113.080, 125.706, 119.183, 120.966, 122.361,
126.675, 117.069, 120.875, 109.372, 119.811, 126.048]
i = 0
@@ -3020,7 +3020,7 @@
if curspin.select == False:
j += 1
- # Test number of selected/deselected spins.
+ # Test number of selected/deselected spins.
self.assertEqual(i, len(cluster_ids))
self.assertEqual(j, 48-len(cluster_ids))
@@ -3158,7 +3158,7 @@
self.interpreter.relax_disp.cluster('free spins', curspin)
# Shut them down
self.interpreter.deselect.spin(spin_id=curspin,
change_all=False)
-
+
# Select only a subset of spins for global fitting
#self.interpreter.select.spin(spin_id=':41@N', change_all=False)
#self.interpreter.relax_disp.cluster('model_cluster', ':41@N')
@@ -3571,7 +3571,7 @@
User function to set the R20 parameters in the default grid search
using the minimum R2eff value.
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
'SOD1-WT' CPMG data to the CR72 dispersion model.
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
@@ -3594,8 +3594,8 @@
# Change pipe.
pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL)
- self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
- self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
+ self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
+ self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
# Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
@@ -3663,7 +3663,7 @@
### Then test the value.set function.
# Change pipe.
pipe_name_MODEL = "%s_%s_2"%(pipe_name, MODEL)
- self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
+ self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
# Then select model.
@@ -3718,7 +3718,7 @@
def test_sod1wt_t25_bug_21954_order_error_analysis(self):
"""Error analysis of SOD1-WT CPMG. From paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}.
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
'SOD1-WT' CPMG data to the CR72 dispersion model.
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
@@ -3748,8 +3748,8 @@
spectrum_ids_B.append(spectrum_id)
# To clean up old error analysis, delete attributes
- delattr(cdp, "var_I")
- delattr(cdp, "sigma_I")
+ delattr(cdp, "var_I")
+ delattr(cdp, "sigma_I")
# Perform error analysis
self.interpreter.spectrum.error_analysis(subset=spectrum_ids_A)
@@ -3758,13 +3758,13 @@
# Loop over spins, save errors to list
Errors_A_B = []
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
- A_err = spin.peak_intensity_err[spectrum_ids_A[0]]
- B_err = spin.peak_intensity_err[spectrum_ids_B[0]]
+ A_err = spin.peak_intensity_err[spectrum_ids_A[0]]
+ B_err = spin.peak_intensity_err[spectrum_ids_B[0]]
Errors_A_B.append([A_err, B_err])
# To clean up old error analysis, delete attributes
- delattr(cdp, "var_I")
- delattr(cdp, "sigma_I")
+ delattr(cdp, "var_I")
+ delattr(cdp, "sigma_I")
# Perform error analysis. Order is important
self.interpreter.spectrum.error_analysis(subset=spectrum_ids_B)
@@ -3773,8 +3773,8 @@
# Loop over spins, save errors to list
Errors_B_A = []
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
- A_err = spin.peak_intensity_err[spectrum_ids_A[0]]
- B_err = spin.peak_intensity_err[spectrum_ids_B[0]]
+ A_err = spin.peak_intensity_err[spectrum_ids_A[0]]
+ B_err = spin.peak_intensity_err[spectrum_ids_B[0]]
Errors_B_A.append([A_err, B_err])
# Make test for order of error
@@ -3803,7 +3803,7 @@
def test_sod1wt_t25_to_cr72(self):
"""Optimisation of SOD1-WT CPMG. From paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}.
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
'SOD1-WT' CPMG data to the CR72 dispersion model.
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
@@ -3826,8 +3826,8 @@
# Change pipe.
pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL)
- self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
- self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
+ self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL)
+ self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL)
# Then select model.
self.interpreter.relax_disp.select_model(model=MODEL)
@@ -3887,7 +3887,7 @@
## Prepare for clustering
# Change pipe.
pipe_name_MODEL_CLUSTER = "%s_%s_Cluster"%(pipe_name, MODEL)
- self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL_CLUSTER)
+ self.interpreter.pipe.copy(pipe_from=pipe_name_r2eff,
pipe_to=pipe_name_MODEL_CLUSTER)
self.interpreter.pipe.switch(pipe_name=pipe_name_MODEL_CLUSTER)
# Then select model.
@@ -3971,7 +3971,7 @@
def test_sod1wt_t25_to_sherekhan_input(self):
"""Conversion of SOD1-WT CPMG R2eff values into input files for
sherekhan.
- Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
+ Optimisation of Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C.
Christensen, Gleb Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
'SOD1-WT' CPMG data to the CR72 dispersion model.
This uses the data from paper at
U{http://dx.doi.org/10.1073/pnas.0907387106}. This is CPMG data with a fixed
relaxation time period recorded at fields of 500 and 600MHz.
r22924 - /trunk/test_suite/system_tests/relax_disp.py