Author: bugman
Date: Wed Nov 14 17:21:07 2012
New Revision: 17970
URL: http://svn.gna.org/viewcvs/relax?rev=17970&view=rev
Log:
Created the N_state_model.test_data_copying system test for the rdc.copy and
pcs.copy user functions.
These user functions do not exist yet, but this test will be used to
implement them.
Added:
trunk/test_suite/system_tests/scripts/n_state_model/data_copying.py
- copied, changed from r17959,
trunk/test_suite/system_tests/scripts/n_state_model/populations.py
Modified:
trunk/test_suite/system_tests/n_state_model.py
Modified: trunk/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/n_state_model.py?rev=17970&r1=17969&r2=17970&view=diff
==============================================================================
--- trunk/test_suite/system_tests/n_state_model.py (original)
+++ trunk/test_suite/system_tests/n_state_model.py Wed Nov 14 17:21:07 2012
@@ -31,6 +31,7 @@
from generic_fns.align_tensor import calc_chi_tensor
from generic_fns.interatomic import interatomic_loop, return_interatom
from generic_fns.mol_res_spin import return_spin, spin_loop
+from generic_fns.pipes import get_pipe
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -379,6 +380,22 @@
self.assertAlmostEqual(cdp.q_rdc_norm2, 0.14049691097282743) #
Pales (Q RDC_RMS): 0.141
+ def test_data_copying(self):
+ """The copying of RDC and PCS data from one pipe to another."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'data_copying.py')
+
+ # Get the data pipes.
+ orig = get_pipe('orig')
+ new = get_pipe('new')
+
+ # Check the data.
+ self.assertEqual(orig.rdc_ids, new.rdc_ids)
+ self.assertEqual(orig.pcs_ids, new.pcs_ids)
+ self.assertEqual(orig.align_ids, new.align_ids)
+
+
def test_lactose_n_state_fixed(self):
"""The 4-state model analysis of lactose using RDCs and PCSs."""
Copied: trunk/test_suite/system_tests/scripts/n_state_model/data_copying.py
(from r17959,
trunk/test_suite/system_tests/scripts/n_state_model/populations.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/data_copying.py?p2=trunk/test_suite/system_tests/scripts/n_state_model/data_copying.py&p1=trunk/test_suite/system_tests/scripts/n_state_model/populations.py&r1=17959&r2=17970&rev=17970&view=diff
==============================================================================
--- trunk/test_suite/system_tests/scripts/n_state_model/populations.py
(original)
+++ trunk/test_suite/system_tests/scripts/n_state_model/data_copying.py Wed
Nov 14 17:21:07 2012
@@ -13,7 +13,7 @@
data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'population_model'
# Create the data pipe.
-self._execute_uf(uf_name='pipe.create', pipe_name='populations',
pipe_type='N-state')
+self._execute_uf(uf_name='pipe.create', pipe_name='orig',
pipe_type='N-state')
# Load the structures.
NUM_STR = 3
@@ -32,14 +32,14 @@
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H17')
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H18')
-# Define the magnetic dipole-dipole relaxation interaction.
-self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
-self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@C*',
spin_id2='@H*', ave_dist=1.10 * 1e-10)
-self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-
-# Set the nuclear isotope type.
-self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
-self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
+## Define the magnetic dipole-dipole relaxation interaction.
+#self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
+#self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@C*',
spin_id2='@H*', ave_dist=1.10 * 1e-10)
+#self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
+#
+## Set the nuclear isotope type.
+#self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+#self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# File list.
align_list = ['Dy', 'Tb', 'Tm', 'Er']
@@ -59,39 +59,9 @@
# The frequency.
self._execute_uf(uf_name='frq.set', id=align_list[i], frq=799.75376122 *
1e6)
-# Set the paramagnetic centre.
-self._execute_uf(uf_name='paramag.centre', pos=[ -14.845, 0.969,
0.265])
+# Create a new data pipe.
+self._execute_uf(uf_name='pipe.create', pipe_name='new', pipe_type='N-state')
-
-# The solution.
-###############
-
-# Set up the model.
-self._execute_uf(uf_name='n_state_model.select_model', model='population')
-
-# Set pc to the exact values.
-self._execute_uf(uf_name='value.set', val=0.3, param='p0')
-self._execute_uf(uf_name='value.set', val=0.1, param='p2')
-self._execute_uf(uf_name='value.set', val=0.6, param='p1')
-
-# Set the tensors.
-self._execute_uf(uf_name='align_tensor.init', tensor=align_list[0], params=(
1.42219822168827662867e-04, -1.44543001566521341940e-04,
-7.07796211648713973798e-04, -6.01619494082773244303e-04,
2.02008007072950861996e-04), param_types=2)
-self._execute_uf(uf_name='align_tensor.init', tensor=align_list[1], params=(
3.56720663040924505435e-04, -2.68385787902088840916e-04,
-1.69361406642305853832e-04, 1.71873715515064501074e-04,
-3.05790155096090983822e-04), param_types=2)
-self._execute_uf(uf_name='align_tensor.init', tensor=align_list[2], params=(
2.32088908680377300801e-07, 2.08076808579168379617e-06,
-2.21735465435989729223e-06, -3.74311563209448033818e-06,
-2.40784858070560310370e-06), param_types=2)
-self._execute_uf(uf_name='align_tensor.init', tensor=align_list[3],
params=(-2.62495279588228071048e-04, 7.35617367964106275147e-04,
6.39754192258981332648e-05, 6.27880171180572523460e-05,
2.01197582457700226708e-04), param_types=2)
-
-# Calculation.
-self._execute_uf(uf_name='calc')
-print("Chi2: %s" % cdp.chi2)
-if abs(cdp.chi2) > 1e-15:
- raise RelaxError("The chi2 at the solution is not zero!")
-
-
-# The population model opt.
-###########################
-
-# Minimisation.
-self._execute_uf(uf_name='minimise', min_algor='sd', func_tol=1e-2)
-
-# Write out a results file.
-self._execute_uf(uf_name='results.write', file='devnull', force=True)
+# Copy the data.
+self._execute_uf(uf_name='rdc.copy', pipe_from='orig', pipe_to='new')
+self._execute_uf(uf_name='pcs.copy', pipe_from='orig', pipe_to='new')
r17970 - in /trunk/test_suite/system_tests: n_state_model.py scripts/n_state_model/data_copying.py