Author: bugman
Date: Thu Jun 21 10:22:21 2012
New Revision: 17016
URL: http://svn.gna.org/viewcvs/relax?rev=17016&view=rev
Log:
Many fixes for the model-free system tests and related data.
Now all model-free tests pass under the new interatomic data design.
Modified:
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2
branches/interatomic/test_suite/system_tests/model_free.py
branches/interatomic/test_suite/system_tests/scripts/model_free/omp_model_free.py
Modified:
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_pre_py2.7.3_v2.bz2?rev=17016&r1=17015&r2=17016&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2.bz2?rev=17016&r1=17015&r2=17016&view=diff
==============================================================================
Binary files - no diff available.
Modified:
branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3_v2_broken.bz2?rev=17016&r1=17015&r2=17016&view=diff
==============================================================================
Binary files - no diff available.
Modified: branches/interatomic/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/model_free.py?rev=17016&r1=17015&r2=17016&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/model_free.py (original)
+++ branches/interatomic/test_suite/system_tests/model_free.py Thu Jun 21
10:22:21 2012
@@ -310,7 +310,7 @@
isotopes = ["15N", "1H"] * 9
csa = [-172e-6, None] * 9
select = [True, False] * 9
- fixed = [False, None] * 9
+ fixed = [False, False] * 9
s2 = [0.8, None] * 9
te = [20e-12, None] * 9
@@ -397,8 +397,8 @@
# Load the relaxation data.
for i in range(len(frq)):
self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE',
float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
- self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1',
float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
- self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2',
float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
+ self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1',
float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2',
float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
# Set up the initial model-free parameter values (bypass the grid
search for speed).
self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2',
'te'])
@@ -424,9 +424,9 @@
# Load the relaxation data.
for i in range(len(frq)):
- self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE',
float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
- self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1',
float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
- self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2',
float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4)
+ self.interpreter.relax_data.read('NOE_%s'%frq[i], 'NOE',
float(frq[i])*1e6, 'noe.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R1_%s'%frq[i], 'R1',
float(frq[i])*1e6, 'r1.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R2_%s'%frq[i], 'R2',
float(frq[i])*1e6, 'r2.%s.out' % frq[i], dir=cdp.path, res_num_col=1,
res_name_col=2, data_col=3, error_col=4, spin_id='@N')
# Set up the initial model-free parameter values (bypass the grid
search for speed).
self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2',
'te'])
@@ -448,15 +448,15 @@
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_local_tm_10_S2_0_8_te_40.py')
# Load the relaxation data.
- self.interpreter.relax_data.read('R2_700', 'R2', 700*1e6,
'r2.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('NOE_500', 'NOE', 500*1e6,
'noe.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('R1_500', 'R1', 500*1e6,
'r1.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('R1_900', 'R1', 900*1e6,
'r1.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('NOE_900', 'NOE', 900*1e6,
'noe.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('R2_900', 'R2', 900*1e6,
'r2.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('R1_700', 'R1', 700*1e6,
'r1.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('NOE_700', 'NOE', 700*1e6,
'noe.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- self.interpreter.relax_data.read('R2_500', 'R2', 500*1e6,
'r2.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
+ self.interpreter.relax_data.read('R2_700', 'R2', 700*1e6,
'r2.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('NOE_500', 'NOE', 500*1e6,
'noe.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R1_500', 'R1', 500*1e6,
'r1.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R1_900', 'R1', 900*1e6,
'r1.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('NOE_900', 'NOE', 900*1e6,
'noe.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R2_900', 'R2', 900*1e6,
'r2.900.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R1_700', 'R1', 700*1e6,
'r1.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('NOE_700', 'NOE', 700*1e6,
'noe.700.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
+ self.interpreter.relax_data.read('R2_500', 'R2', 500*1e6,
'r2.500.out', dir=cdp.path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4, spin_id='@N')
# Set up the initial model-free parameter values (bypass the grid
search for speed).
self.interpreter.value.set([15.0e-9, 1.0, 0.0], ['local_tm', 's2',
'te'])
@@ -720,8 +720,9 @@
self.interpreter.relax_data.read('R2_500', 'R2', 500.0*1e6,
'r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
self.interpreter.relax_data.read('NOE_500', 'NOE', 500.0*1e6,
'noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
- # Name the spins.
+ # Name the spins and set the element type.
self.interpreter.spin.name('N')
+ self.interpreter.spin.element('N')
# Create all attached protons.
self.interpreter.sequence.attach_protons()
@@ -1992,6 +1993,9 @@
# Aliases
res = cdp.mol[0].res[i]
spin = cdp.mol[0].res[i].spin[0]
+ h_spin = None
+ if len(cdp.mol[0].res[i].spin) > 1:
+ h_spin = cdp.mol[0].res[i].spin[1]
# Debugging printout.
print(res)
@@ -2001,18 +2005,24 @@
self.assertEqual(res.num, num[i])
self.assertEqual(res.name, 'XXX')
self.assertEqual(spin.num, None)
- self.assertEqual(spin.name, None)
+ if select[i]:
+ self.assertEqual(spin.name, 'N')
+ self.assertEqual(spin.fixed, False)
+ else:
+ self.assertEqual(spin.name, None)
self.assertEqual(spin.select, select[i])
- self.assertEqual(spin.fixed, False)
+ if h_spin:
+ self.assertEqual(h_spin.num, None)
+ self.assertEqual(h_spin.name, 'H')
+ self.assertEqual(h_spin.select, False)
# Skip deselected spins.
if not select[i]:
continue
- # Structural info.
- self.assertEqual(spin.heteronuc_type, '15N')
- self.assertEqual(spin.proton_type, '1H')
- self.assertEqual(spin.attached_proton, None)
+ # Nuclear isotope info.
+ self.assertEqual(spin.isotope, '15N')
+ self.assertEqual(h_spin.isotope, '1H')
# Model-free tests.
self.assertEqual(spin.model, model[j])
@@ -2030,7 +2040,6 @@
if rex[j] != None:
rex[j] = rex[j]/(2.0*pi*500000000.0)**2
self.assertEqual(spin.rex, rex[j])
- self.assertEqual(spin.r, 1.0200000000000001e-10)
self.assertEqual(spin.csa, -0.00016999999999999999)
# Minimisation statistic tests.
@@ -2049,6 +2058,10 @@
# Secondary index.
j = j + 1
+
+ # The interatomic data tests.
+ for i in range(len(cdp.interatomic)):
+ self.assertEqual(cdp.interatomic[i].r, 1.0200000000000001e-10)
def test_read_results_1_2_pse4(self):
@@ -2162,7 +2175,7 @@
self.assertEqual(h_spin.name, 'H')
self.assertEqual(h_spin.select, False)
- # Structural info.
+ # Nuclear isotope info.
self.assertEqual(spin.isotope, '15N')
self.assertEqual(h_spin.isotope, '1H')
@@ -2313,7 +2326,7 @@
self.assertEqual(h_spin.name, 'H')
self.assertEqual(h_spin.select, False)
- # Structural info.
+ # Nuclear isotope info.
self.assertEqual(spin.isotope, '15N')
self.assertEqual(h_spin.isotope, '1H')
@@ -2443,8 +2456,8 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['s2', 'te',
'rex'])
- def test_set_bond_length(self):
- """Setting the bond length through the user function value.set()."""
+ def test_set_csa(self):
+ """Setting the CSA value through the user function value.set()."""
# Path of the files.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149'
@@ -2453,43 +2466,10 @@
self.interpreter.sequence.read(file='noe.500.out', dir=path,
res_num_col=1, res_name_col=2)
# Set the CSA value.
- self.interpreter.value.set(NH_BOND_LENGTH, 'r')
-
- # Test the value.
- self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)
-
-
- def test_set_csa(self):
- """Setting the CSA value through the user function value.set()."""
-
- # Path of the files.
- path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149'
-
- # Read the sequence.
- self.interpreter.sequence.read(file='noe.500.out', dir=path,
res_num_col=1, res_name_col=2)
-
- # Set the CSA value.
self.interpreter.value.set(N15_CSA, 'csa')
# Test the value.
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA)
-
-
- def test_set_csa_bond_length(self):
- """Setting both the CSA value and bond length through the user
function value.set()."""
-
- # Path of the files.
- path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149'
-
- # Read the sequence.
- self.interpreter.sequence.read(file='noe.500.out', dir=path,
res_num_col=1, res_name_col=2)
-
- # Set the CSA value and bond length simultaneously.
- self.interpreter.value.set([N15_CSA, NH_BOND_LENGTH], ['csa', 'r'])
-
- # Test the values.
- self.assertEqual(cdp.mol[0].res[1].spin[0].csa, N15_CSA)
- self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)
def test_tm0_grid(self):
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/omp_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/omp_model_free.py?rev=17016&r1=17015&r2=17016&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/omp_model_free.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/omp_model_free.py
Thu Jun 21 10:22:21 2012
@@ -211,7 +211,6 @@
# Define the magnetic dipole-dipole relaxation interaction.
dipole_pair.define(spin_id1='@N', spin_id2='@H',
direct_bond=True)
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02
* 1e-10)
- dipole_pair.unit_vectors()
# Set all the necessary values.
value.set(CSA, 'csa')
r17016 - in /branches/interatomic/test_suite: shared_data/model_free/OMP/ system_tests/ system_tests/scripts/model_free/