Author: tlinnet
Date: Tue Apr 22 20:48:30 2014
New Revision: 22828
URL: http://svn.gna.org/viewcvs/relax?rev=22828&view=rev
Log:
Splitted systemtest Relax_disp.sod1wt_t25_to_cr72 into part as setup and test
part.
Regarding bug #21953, (https://gna.org/bugs/index.php?21953) - Weird
performance of grid search
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=22828&r1=22827&r2=22828&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Apr 22 20:48:30 2014
@@ -240,6 +240,130 @@
# Change the model.
self.interpreter.relax_disp.select_model('NS MMQ 2-site')
+
+
+ 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
+ '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.
+ Data is for experiment at 25 degree Celcius.
+ """
+
+ # Create the data pipe and load the base data.
+ data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'sod1wt_t25'
+
+ # Set experiment settings. sfrq, time_T2, ncyc
+ Exps = [
+ ["600MHz", "Z_A", 599.8908617*1E6, 0.06, [28, 0, 4, 32, 60, 2, 10,
16, 8, 20, 50, 18, 40, 6, 12, 0, 24], ["Z_A1", "Z_A15"] ],
+ ["500MHz", "Z_B", 499.862139*1E6, 0.04, [20, 0, 16, 10, 36, 2, 12,
4, 22, 18, 40, 14, 26, 8, 32, 24, 6, 28, 0], ["Z_B1", "Z_B18"] ] ]
+
+ # Create base pipe
+ self.interpreter.pipe.create(pipe_name=pipe_name,
pipe_type=pipe_type)
+
+ # Loop throug experiments
+ id_lists = []
+ for folder, key, sfrq, time_T2, ncycs, rep_ncyss in Exps:
+ # Read spins
+ self.interpreter.spectrum.read_spins(file="128_FT.ser",
dir=data_path+sep+folder)
+ self.interpreter.spectrum.read_spins(file="128_FT.ser",
dir=data_path+sep+folder)
+
+ # Make spectrum id list
+ id_list = list(key+str(i) for i in range(len(ncycs)))
+ id_lists.append(id_list)
+
+ # Read intensities
+ self.interpreter.spectrum.read_intensities(file="128_FT.ser",
dir=data_path+sep+folder, int_method='height', spectrum_id=id_list,
int_col=list(xrange(len(id_list))) )
+
+ # Loop over experiments
+ for i in range(len(ncycs)):
+ ncyc = ncycs[i]
+ vcpmg = ncyc/time_T2
+
+ # 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.
+ self.interpreter.relax_disp.exp_type(spectrum_id=current_id,
exp_type='SQ CPMG')
+
+ # 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).
+
self.interpreter.relax_disp.relax_time(spectrum_id=current_id, time=time_T2)
+
+ # Set the relaxation dispersion CPMG frequencies.
+ self.interpreter.relax_disp.cpmg_frq(spectrum_id=current_id,
cpmg_frq=vcpmg)
+
+ # Define replicated
+ self.interpreter.spectrum.replicated(spectrum_ids=Exps[0][5])
+ self.interpreter.spectrum.replicated(spectrum_ids=Exps[1][5])
+
+ # Perform error analysis
+ self.interpreter.spectrum.error_analysis(subset=id_lists[0])
+ self.interpreter.spectrum.error_analysis(subset=id_lists[1])
+
+ # Define isotope
+ self.interpreter.spin.isotope(isotope='15N')
+
+ #############
+
+ # 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",
+ "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
+ self.assertEqual(64, len(glob_assn ))
+
+ ## Turn assignments into relax spin ids.
+ # Define regular expression search
+ r = re.compile("([a-zA-Z]+)([0-9]+)([a-zA-Z]+)")
+
+ # Create list to hold regular expression search
+ relax_glob_ids = []
+
+ # Loop over assignments
+ for assn in glob_assn:
+ # Make match for the regular search
+ m = r.match(assn)
+ # Convert to relax spin string
+ relax_string = ":%s@%s"%(m.group(2),m.group(3))
+
+ # Save the relax spin string and the regular search
+ relax_glob_ids.append([m.group(0), m.group(1), m.group(2),
m.group(3), relax_string])
+
+ ############# Deselect all spins, and select few spins
+
+ ## Deselect all spins, and select a few for analysis
+ self.interpreter.deselect.all()
+
+ # Select few spins
+ for i in select_spin_index:
+ self.interpreter.select.spin(spin_id=relax_glob_ids[i][4],
change_all=False)
+
+ ##############
+
+ # 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)
+
+ # Select model for points calculation
+ MODEL = "R2eff"
+ self.interpreter.relax_disp.select_model(model=MODEL)
+ # Calculate R2eff values
+ self.interpreter.calc(verbosity=1)
def test_bug_21081_disp_cluster_fail(self):
@@ -3447,126 +3571,16 @@
Data is for experiment at 25 degree Celcius.
"""
- # Create the data pipe and load the base data.
- data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'sod1wt_t25'
-
- # Set experiment settings. sfrq, time_T2, ncyc
- Exps = [
- ["600MHz", "Z_A", 599.8908617*1E6, 0.06, [28, 0, 4, 32, 60, 2, 10,
16, 8, 20, 50, 18, 40, 6, 12, 0, 24], ["Z_A1", "Z_A15"] ],
- ["500MHz", "Z_B", 499.862139*1E6, 0.04, [20, 0, 16, 10, 36, 2, 12,
4, 22, 18, 40, 14, 26, 8, 32, 24, 6, 28, 0], ["Z_B1", "Z_B18"] ] ]
-
- # Generate r20 keu
- r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=Exps[0][2])
- r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=Exps[1][2])
-
- # Create base pipe
+ # Base data setup.
pipe_name = 'base pipe'
pipe_type = 'relax_disp'
- self.interpreter.pipe.create(pipe_name=pipe_name,
pipe_type=pipe_type)
-
- # Loop throug experiments
- id_lists = []
- for folder, key, sfrq, time_T2, ncycs, rep_ncyss in Exps:
- # Read spins
- self.interpreter.spectrum.read_spins(file="128_FT.ser",
dir=data_path+sep+folder)
- self.interpreter.spectrum.read_spins(file="128_FT.ser",
dir=data_path+sep+folder)
-
- # Make spectrum id list
- id_list = list(key+str(i) for i in range(len(ncycs)))
- id_lists.append(id_list)
-
- # Read intensities
- self.interpreter.spectrum.read_intensities(file="128_FT.ser",
dir=data_path+sep+folder, int_method='height', spectrum_id=id_list,
int_col=list(xrange(len(id_list))) )
-
- # Loop over experiments
- for i in range(len(ncycs)):
- ncyc = ncycs[i]
- vcpmg = ncyc/time_T2
-
- # 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.
- self.interpreter.relax_disp.exp_type(spectrum_id=current_id,
exp_type='SQ CPMG')
-
- # 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).
-
self.interpreter.relax_disp.relax_time(spectrum_id=current_id, time=time_T2)
-
- # Set the relaxation dispersion CPMG frequencies.
- self.interpreter.relax_disp.cpmg_frq(spectrum_id=current_id,
cpmg_frq=vcpmg)
-
- # Define replicated
- self.interpreter.spectrum.replicated(spectrum_ids=Exps[0][5])
- self.interpreter.spectrum.replicated(spectrum_ids=Exps[1][5])
-
- # Perform error analysis
- self.interpreter.spectrum.error_analysis(subset=id_lists[0])
- self.interpreter.spectrum.error_analysis(subset=id_lists[1])
- #self.interpreter.spectrum.error_analysis(subset=id_lists[0])
-
- # Define isotope
- self.interpreter.spin.isotope(isotope='15N')
-
- #############
-
- # 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",
- "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
- self.assertEqual(64, len(glob_assn ))
-
- ## Turn assignments into relax spin ids.
- # Define regular expression search
- r = re.compile("([a-zA-Z]+)([0-9]+)([a-zA-Z]+)")
-
- # Create list to hold regular expression search
- relax_glob_ids = []
-
- # Loop over assignments
- for assn in glob_assn:
- # Make match for the regular search
- m = r.match(assn)
- # Convert to relax spin string
- relax_string = ":%s@%s"%(m.group(2),m.group(3))
-
- # Save the relax spin string and the regular search
- relax_glob_ids.append([m.group(0), m.group(1), m.group(2),
m.group(3), relax_string])
-
- ############# Deselect all spins, and select few spins
-
- ## Deselect all spins, and select a few for analysis
- self.interpreter.deselect.all()
-
- # Select few spins
- for i in range(0,2):
- self.interpreter.select.spin(spin_id=relax_glob_ids[i][4],
change_all=False)
-
- ##############
-
- # Prepare for R2eff calculation
pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- 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"
- self.interpreter.relax_disp.select_model(model=MODEL)
- # Calculate R2eff values
- self.interpreter.calc(verbosity=1)
+ select_spin_index = range(0,2)
+ self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
+
+ # Generate r20 keu
+ r20_key_600 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=599.8908617*1E6)
+ r20_key_500 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ,
frq=499.862139*1E6)
## Now prepare for MODEL calculation
MODEL = "CR72"
r22828 - /trunk/test_suite/system_tests/relax_disp.py