Author: tlinnet
Date: Mon Apr 21 21:23:54 2014
New Revision: 22811
URL: http://svn.gna.org/viewcvs/relax?rev=22811&view=rev
Log:
Added systemtest to analyse data.
Systemtest for CPMG dataset, (http://dx.doi.org/10.1073/pnas.0907387106)
Kaare Teilum, Melanie H. Smith, Eike Schulz, Lea C. Christensen, Gleb
Solomentseva, Mikael Oliveberg, and Mikael Akkea 2009
SOD1-WT at 25 C.
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=22811&r1=22810&r2=22811&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Apr 21 21:23:54 2014
@@ -23,6 +23,8 @@
# Python module imports.
from os import F_OK, access, sep
+import re
+import time
from tempfile import mkdtemp
# relax module imports.
@@ -2364,6 +2366,182 @@
self.assertAlmostEqual(res61L.k_AB, 10.55, 0)
+ def
test_kteilum_mhsmith_eschulz_lcchristensen_gsolomentsev_moliveberg_makke_sod1wt_t25_to_cr72(self):
+ """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+'KTeilum_MHsmith_ESchulz_LCchristensen_GSolomentsev_MOliveberg_MAkke_2009'
+
+ # 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
+ 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(1):
+ 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)
+
+ # Save disp grap to temp
+ #self.interpreter.relax_disp.plot_disp_curves(dir="~"+sep+"test",
num_points=1000, extend=500.0, force=True)
+
+ ## Now prepare for MODEL calculation
+ MODEL = "CR72"
+
+ # 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)
+
+ # Then select model
+ self.interpreter.relax_disp.select_model(model=MODEL)
+
+ GRID_INCS = [3, 5]
+ #GRID_INCS = [3, 5, 7, 9, 11, 13, 19, 21]
+ GRID_RESULTS = []
+ for GRID_INC in GRID_INCS:
+ # Measure time
+ start = time.time()
+
+ # Set initial value
+ for spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ spin.kex = 2200.
+
+ # Perform Grid Search
+ self.interpreter.grid_search(lower=None, upper=None,
inc=GRID_INC, constraints=True, verbosity=1)
+
+ # Stop time
+ done = time.time()
+ elapsed = done - start
+
+ # Print info out
+ for spin, mol_name, resi, resn, spin_id in
spin_loop(full_info=True, return_id=True, skip_desel=True):
+ GRID_RESULTS.append([GRID_INC, spin.kex, spin.pA, spin.dw,
spin.r2[r20_key_500], spin.r2[r20_key_600], mol_name, resi, resn, spin_id,
elapsed])
+ # Resetting back to nothing
+ spin.kex, spin.pA, spin.dw, spin.r2[r20_key_500],
spin.r2[r20_key_600] = None, None, None, None, None
+
+ for GRID, kex, pA, dw, r2500, r2600, mol, resi, resn, spin_id,
elapsed in GRID_RESULTS:
+ print("########################## GRID INC %s
##########################"%GRID)
+ print("GRID, kex, pA, dw, r2500, r2600, mol, resi, resn,
spin_id, elapsed")
+ print(GRID, kex, pA, dw, r2500, r2600, mol, resi, resn, spin_id,
elapsed)
+
+ #self.assertAlmostEqual(spin.pA, 0.99)
+ #self.assertAlmostEqual(spin.kex, 2200)
+
+
def test_m61_data_to_m61(self):
"""Test the relaxation dispersion 'M61' model curve fitting to fixed
time synthetic data."""
r22811 - /trunk/test_suite/system_tests/relax_disp.py