Author: bugman
Date: Thu Jan 24 12:51:23 2013
New Revision: 18300
URL: http://svn.gna.org/viewcvs/relax?rev=18300&view=rev
Log:
Merged revisions 18297-18299 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18297 | bugman | 2013-01-24 12:04:27 +0100 (Thu, 24 Jan 2013) | 3 lines
The N_state_model.test_align_fit system test now checks the simulation PCS
values.
........
r18298 | bugman | 2013-01-24 12:42:17 +0100 (Thu, 24 Jan 2013) | 5 lines
Fix for the metal_pos_opt.py N-state model system test script.
The moving interatomic data containers are now also deselected.
........
r18299 | bugman | 2013-01-24 12:42:41 +0100 (Thu, 24 Jan 2013) | 3 lines
Added extensive data checks to the N_state_model.test_metal_pos_opt system
test script.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Jan 24 12:51:23 2013
@@ -1,1 +1,1 @@
-/trunk:1-18295
+/trunk:1-18299
Modified:
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/n_state_model.py?rev=18300&r1=18299&r2=18300&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/n_state_model.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/n_state_model.py Thu
Jan 24 12:51:23 2013
@@ -246,6 +246,10 @@
# Check the back-calculated value.
self.assertAlmostEqual(spin.pcs_bc[tag], pcs[i])
+ # Check the simulation values.
+ for sim_index in range(cdp.sim_number):
+ self.assert_(abs(spin.pcs_sim[tag][sim_index] -
spin.pcs[tag]) < 6.0*spin.pcs_err[tag])
+
# Increment the spin index.
i += 1
@@ -561,6 +565,79 @@
self.assertAlmostEqual(cdp.q_rdc, 0.0)
self.assertAlmostEqual(cdp.q_pcs, 0.0)
+ # The spin data.
+ pcs = {
+ 'Dy': [ 0.257602207272000, 0.068336164014900,
0.110603133551000, 0.283488541078000, 0.339904760907000,
0.987042929223000, 0.442512226783000, 0.369383947069000,
0.576421001305000, 0.414840770458000, 0.332707187464000,
-0.029503579631700, 0.134647155776000, 0.112481223655000,
0.355198596515000, -0.046913037723100, -0.118710220626000,
0.029273074820300, 0.302949891871000, 1.312854817740000,
0.040875625448800, 0.608281919748000, 0.023360076276000,
0.811293913028000, 0.258701382871000, 0.056025797668300,
0.609547727298000, 0.906885191563000],
+ 'Tb': [0.644225239812000, 0.677797993460000,
0.492912191403000, 0.524119985177000, 0.600493382214000, 0.501470795483000,
0.516761193931000, 0.702967176951000, 0.914836321239000, 1.318114995620000,
1.350055099220000, 0.893477362442000, 0.999911636071000, 1.065232203160000,
0.996395971540000, 0.720982749003000, 1.374318729640000, 2.106902457600000],
+ 'Tm': [ 0.000125066528687, -0.000564062193363,
-0.000607973317902, 0.000090266635200, 0.000174865797403,
0.002488010156480, 0.000830246873289, 0.000762523870219,
-0.000096933008248, 0.000742665143642, -0.000215152849719],
+ 'Er': [-0.481445160767000, -0.361046693640000,
-0.370098680342000, -0.413514467402000, -0.410802287329000,
-1.081011578870000, -0.963176128222000, -0.745366702244000,
-0.674570724880000, -0.751320872646000, -0.684906087274000,
-0.461253969271000, -0.443680922437000, -0.344056233315000,
-0.328118573270000, -0.395048353548000, -0.356220572284000,
-0.324533952261000, -0.411777498713000, -0.511811581196000,
-1.018565433020000, -0.959481602761000, -0.734022165690000,
-0.660034918889000, -0.709085634512000, -0.878775632044000,
-0.553464480425000, -0.765371835675000, -1.548006987460000]
+ }
+ # Loop over the align IDs.
+ for tag in ['Dy', 'Tb', 'Tm', 'Er']:
+ i = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Deselected spin.
+ if not spin.select:
+ continue
+
+ # No PCS.
+ if not hasattr(spin, 'pcs'):
+ print("No PCS for spin '%s'." % spin_id)
+ continue
+ if not tag in spin.pcs:
+ print("No PCS for the '%s' alignment ID for spin '%s'."
% (tag, spin_id))
+ continue
+ print("Checking '%s' PCS data for spin '%s'" % (tag,
spin_id))
+
+ # Check the value.
+ self.assertAlmostEqual(spin.pcs[tag], pcs[tag][i])
+
+ # Check the back-calculated value.
+ self.assertAlmostEqual(spin.pcs_bc[tag], pcs[tag][i])
+
+ # Check the simulation values.
+ for sim_index in range(cdp.sim_number):
+ self.assert_(abs(spin.pcs_sim[tag][sim_index] -
spin.pcs[tag]) < 6.0*spin.pcs_err[tag])
+
+ # Increment the spin index.
+ i += 1
+
+ # The interatomic data.
+ rdc = {
+ 'Dy': [-30.671893754700001, -31.307246147099999,
-29.358121961700000, -7.235977742280000, -45.562589405399997,
-42.816624411200003, -41.019354747700000, -25.361318450599999,
-44.1129977796],
+ 'Tm': [-0.057386340972700, -0.045650398398700,
-0.074873514450400, 0.099056143214600, 0.021275817005300,
0.037132036464200, 0.047340390362400, 0.128745838536000,
0.010906407989400],
+ 'Er': [ 22.944150028900001, 23.363231565100001,
25.948323446000000, 6.955380304960000, 1.784067087050000,
7.228324193240000, 8.271072502000001, -7.403618580470000]
+ }
+ # Loop over the align IDs.
+ for tag in ['Dy', 'Tm', 'Er']:
+ i = 0
+ for interatom in interatomic_loop():
+ # Deselected interatomic container.
+ if not interatom.select:
+ continue
+
+ # No RDC.
+ if not hasattr(interatom, 'rdc'):
+ print("No RDC for interatom '%s-%s'." %
(interatom.spin_id1, interatom.spin_id2))
+ continue
+ if not tag in interatom.rdc:
+ print("No RDC for the '%s' alignment ID for interatom
'%s-%s'." % (tag, interatom.spin_id1, interatom.spin_id2))
+ continue
+ print("Checking '%s' RDC data for interatom '%s-%s'" % (tag,
interatom.spin_id1, interatom.spin_id2))
+
+ # Check the value.
+ self.assertAlmostEqual(interatom.rdc[tag], rdc[tag][i])
+
+ # Check the back-calculated value.
+ self.assertAlmostEqual(interatom.rdc_bc[tag], rdc[tag][i])
+
+ # Check the simulation values.
+ for sim_index in range(cdp.sim_number):
+ self.assert_(abs(interatom.rdc_sim[tag][sim_index] -
interatom.rdc[tag]) < 6.0*interatom.rdc_err[tag])
+
+ # Increment the interatom index.
+ i += 1
+
def test_missing_data(self):
"""Test the use of RDCs and PCSs to find the alignment tensor with
missing data."""
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?rev=18300&r1=18299&r2=18300&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Thu Jan 24 12:51:23 2013
@@ -30,16 +30,20 @@
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*',
ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H*',
ave_pos=False)
+# 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)
+
# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H6')
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H7')
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)
+self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@H6')
+self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@H7')
+self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@H17')
+self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@H18')
# Set the nuclear isotope type.
self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
r18300 - in /branches/frame_order_testing: ./ test_suite/system_tests/ test_suite/system_tests/scripts/n_state_model/