Author: tlinnet
Date: Sat May 3 21:35:13 2014
New Revision: 22942
URL: http://svn.gna.org/viewcvs/relax?rev=22942&view=rev
Log:
Implemented systemtest "relax -s Relax_disp.test_baldwin_synthetic -d" for
model B14.
sr #3154: (https://gna.org/support/?3154) Implementation of Baldwin (2014)
B14 model - 2-site exact solution model for all time scales.
"This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#Debugging
"
This proves that the model is correctly implemented, and return same data
which the
Baldwin script created.
The B14 model is explained in: http://wiki.nmr-relax.com/B14.
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=22942&r1=22941&r2=22942&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Sat May 3 21:35:13 2014
@@ -383,8 +383,8 @@
self.interpreter.pipe.create(pipe_name=pipe_name,
pipe_type=pipe_type)
# Generate the sequence.
- self.interpreter.spin.create(res_name='Ala', res_num=1,
spin_name='N')
- self.interpreter.spin.isotope('15N', spin_id='@N')
+ self.interpreter.spin.create(res_name='Ala', res_num=1,
spin_name='H')
+ self.interpreter.spin.isotope('1H', spin_id='@H')
# Build the experiment IDs.
# Number of cpmg cycles (1 cycle = delay/180/delay/delay/180/delay)
@@ -396,7 +396,7 @@
print("\n\nThe experiment IDs are %s." % ids)
# Set up the metadata for the experiments.
- # This value is used in Baldwin.py. It is the Larmor frequency.
+ # This value is used in Baldwin.py. It is the 1H Larmor frequency.
sfrq= 200. * 1E6
# Total time of CPMG block.
@@ -424,7 +424,7 @@
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@H', disp_point_col=1,
data_col=2, error_col=3)
# Check the global data.
data = [
@@ -451,16 +451,17 @@
else:
for id in ids:
self.assertEqual(obj[id], value[id])
+ pass
# Check the spin data.
n_data = [
- [ 50.000000, 10.286255, 1.0],
- [ 100.000000, 10.073083, 1.0],
- [ 200.000000, 9.692746, 1.0],
- [ 250.000000, 9.382441, 1.0],
- [ 500.000000, 6.312396, 1.0],
- [ 1000.000000, 3.957029, 1.0],
- [ 12500.000000, 2.880420, 1.0]
+ [ 50.000000, 10.286255, 0.1],
+ [ 100.000000, 10.073083, 0.1],
+ [ 200.000000, 9.692746, 0.1],
+ [ 250.000000, 9.382441, 0.1],
+ [ 500.000000, 6.312396, 0.1],
+ [ 1000.000000, 3.957029, 0.1],
+ [ 12500.000000, 2.880420, 0.1]
]
for disp_point, value, error in n_data:
id = 'sq_cpmg_200.00000000_0.000_%.3f' % disp_point
@@ -471,7 +472,7 @@
r20_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=sfrq)
## Now prepare for MODEL calculation.
- MODEL = "CR72"
+ MODEL = "B14"
# Change pipe.
pipe_name_MODEL = "%s_%s"%(pipe_name, MODEL)
@@ -486,10 +487,10 @@
mini_results = []
# Set the R20 parameters in the default grid search using the
minimum R2eff value.
- #self.interpreter.relax_disp.set_grid_r20_from_min_r2eff(force=False)
+ self.interpreter.relax_disp.set_grid_r20_from_min_r2eff(force=False)
# The grid search size (the number of increments per dimension).
- GRID_INC = 7
+ GRID_INC = 11
# Perform Grid Search.
self.interpreter.grid_search(lower=None, upper=None, inc=GRID_INC,
constraints=True, verbosity=1)
@@ -497,11 +498,11 @@
# Store result.
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
# Store grid results.
- grid_results.append([spin.r2[r20_key], spin.dw, spin.pA,
spin.kex, spin.chi2, spin_id, resi, resn])
+ grid_results.append([spin.r2a[r20_key], spin.r2b[r20_key],
spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn])
## Now do minimisation.
# Standard parameters are: func_tol=1e-25, grad_tol=None,
max_iter=10000000,
- set_func_tol = 1e-9
+ set_func_tol = 1e-11
set_max_iter = 100000
self.interpreter.minimise(min_algor='simplex',
func_tol=set_func_tol, max_iter=set_max_iter, constraints=True, scaling=True,
verbosity=1)
@@ -510,7 +511,7 @@
kex_values = []
for spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True,
return_id=True, skip_desel=True):
# Store minimisation results.
- mini_results.append([spin.r2[r20_key], spin.dw, spin.pA,
spin.kex, spin.chi2, spin_id, resi, resn])
+ mini_results.append([spin.r2a[r20_key], spin.r2b[r20_key],
spin.dw, spin.pA, spin.kex, spin.chi2, spin_id, resi, resn])
# Store pA values.
pA_values.append(spin.pA)
@@ -523,11 +524,11 @@
# Print results.
for i in range(len(grid_results)):
# Get values.
- g_r2, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi, g_resn =
grid_results[i]
- m_r2, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi, m_resn =
mini_results[i]
-
- print("GRID r2=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f
spin_id=%s resi=%i resn=%s"%(g_r2, g_dw, g_pA, g_kex, g_chi2, g_spin_id,
g_resi, g_resn))
- print("MIN r2=%2.2f dw=%1.1f pA=%1.3f kex=%3.2f chi2=%3.2f
spin_id=%s resi=%i resn=%s"%(m_r2, m_dw, m_pA, m_kex, m_chi2, m_spin_id,
m_resi, m_resn))
+ g_r2a, g_r2b, g_dw, g_pA, g_kex, g_chi2, g_spin_id, g_resi,
g_resn = grid_results[i]
+ m_r2a, m_r2b, m_dw, m_pA, m_kex, m_chi2, m_spin_id, m_resi,
m_resn = mini_results[i]
+
+ print("GRID r2a=%2.4f r2b=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f
chi2=%3.4f spin_id=%s resi=%i resn=%s"%(g_r2a, g_r2b, g_dw, g_pA, g_kex,
g_chi2, g_spin_id, g_resi, g_resn))
+ print("MIN r2b=%2.4f r2b=%2.4f dw=%1.4f pA=%1.4f kex=%3.4f
chi2=%3.4f spin_id=%s resi=%i resn=%s"%(m_r2a, m_r2b, m_dw, m_pA, m_kex,
m_chi2, m_spin_id, m_resi, m_resn))
# Reference values from Baldwin.py.
# Exchange rate = k+ + k- (s-1)
@@ -541,10 +542,15 @@
#relaxation rate of excited (s-1)
R2e=100.
- #self.assertEqual(cdp.mol[0].res[0].spin[0].kex, kex)
- self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pA, 1-pb, 2)
- #self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2[r20_key], R2g,
2)
- #self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].dw, dw_ppm, 2)
+ # Test the parameters which created the data.
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].kex, kex, 2)
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].pA, 1-pb, 6)
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2a[r20_key], R2g,
4)
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].r2b[r20_key], R2e,
2)
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].dw, dw_ppm, 6)
+
+ # Save graphs
+
#self.interpreter.relax_disp.plot_disp_curves(dir=path.join(getcwd()),
num_points=20, extend=0.0, force=True)
def test_bug_21081_disp_cluster_fail(self):
r22942 - /trunk/test_suite/system_tests/relax_disp.py