Author: bugman
Date: Sun Jun 16 10:15:48 2013
New Revision: 20140
URL: http://svn.gna.org/viewcvs/relax?rev=20140&view=rev
Log:
Merged revisions 20135-20136,20139 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20135 | bugman | 2013-06-14 19:07:31 +0200 (Fri, 14 Jun 2013) | 3 lines
The RDC back-calculation function now supports T = J+D values.
........
r20136 | bugman | 2013-06-14 19:13:56 +0200 (Fri, 14 Jun 2013) | 5 lines
Created the N_state_model.test_absolute_T system test.
This is for checking the optimisation of absolute T=J+D values to find
alignment tensors.
........
r20139 | bugman | 2013-06-16 10:14:01 +0200 (Sun, 16 Jun 2013) | 3 lines
Epydoc docstring fix for the RelaxTestResult.write_time() method.
........
Added:
branches/relax_disp/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
- copied unchanged from r20139,
trunk/test_suite/shared_data/align_data/one_bond_RDC_data_strychnine.txt
branches/relax_disp/test_suite/system_tests/scripts/n_state_model/absolute_T.py
- copied unchanged from r20139,
trunk/test_suite/system_tests/scripts/n_state_model/absolute_T.py
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/rdc.py
branches/relax_disp/test_suite/relax_test_runner.py
branches/relax_disp/test_suite/system_tests/n_state_model.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Sun Jun 16 10:15:48 2013
@@ -1,1 +1,1 @@
-/trunk:1-20133
+/trunk:1-20139
Modified: branches/relax_disp/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/rdc.py?rev=20140&r1=20139&r2=20140&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/rdc.py (original)
+++ branches/relax_disp/pipe_control/rdc.py Sun Jun 16 10:15:48 2013
@@ -118,6 +118,13 @@
for id in align_ids:
# The signed value.
interatom.rdc_bc[id] = ave_rdc_tensor(dj, unit_vect, cdp.N,
cdp.align_tensors[get_tensor_index(align_id=id)].A, weights=weights)
+
+ # T values.
+ if align_id in cdp.rdc_data_types and
cdp.rdc_data_types[align_id] == 'T':
+ if not hasattr(interatom, 'j_coupling'):
+ raise RelaxNoJError
+
+ interatom.rdc_bc[id] += interatom.j_coupling
# The absolute value.
if hasattr(interatom, 'absolute_rdc') and id in
interatom.absolute_rdc.keys() and interatom.absolute_rdc[id]:
Modified: branches/relax_disp/test_suite/relax_test_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/relax_test_runner.py?rev=20140&r1=20139&r2=20140&view=diff
==============================================================================
--- branches/relax_disp/test_suite/relax_test_runner.py (original)
+++ branches/relax_disp/test_suite/relax_test_runner.py Sun Jun 16 10:15:48
2013
@@ -156,8 +156,8 @@
def write_time(self, test_name):
"""Write the timing of the test to the stream.
- @param test: The TestCase name.
- @type test: str
+ @param test_name: The TestCase name.
+ @type test_name: str
"""
# Subtract the end time from the start time.
Modified: branches/relax_disp/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/n_state_model.py?rev=20140&r1=20139&r2=20140&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/n_state_model.py (original)
+++ branches/relax_disp/test_suite/system_tests/n_state_model.py Sun Jun 16
10:15:48 2013
@@ -213,6 +213,65 @@
self.assertAlmostEqual(cdp.q_rdc_norm2, 0.81262759306400001)
+ def test_absolute_T(self):
+ """Test the fitting of signless T values (J+D)."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'absolute_T.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -1.436586299657e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, -5.004443735044e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -5.017832275009e-05)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 1.366097786433e-04)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -1.614772175671e-04)
+ self.assertAlmostEqual(cdp.chi2, 311.70348701353225)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+ self.assertAlmostEqual(cdp.q_rdc_norm2, 0.086891848854541404)
+
+ # The signless T data.
+ T = [195.2, 205.9, 109.4, 113.8, 127.4, 156.0, 92.1, 173.2, 183.0,
174.3, 152.2, 97.3, 136.0, 129.2, 145.5, 156.0, 121.6, 128.0, 154.5, 94.2]
+ T_bc = [
+ 195.009353539915281,
+ 205.456622836526037,
+ 112.285085032859712,
+ 113.628896345578610,
+ 127.440986667041187,
+ 155.505017063790831,
+ 94.332271833299316,
+ 172.408496922639102,
+ 181.972859458051403,
+ 173.655640981746103,
+ 153.402585241137388,
+ 92.115389822570464,
+ 139.743303992644570,
+ 131.399101601878243,
+ 146.219317894376132,
+ 153.945261372587538,
+ 119.541444938794172,
+ 126.620471670822312,
+ 155.940753902549545,
+ 90.813638474619523
+ ]
+
+ # Back calc.
+ self.interpreter.rdc.back_calc('Gel')
+
+ # Check the spin data.
+ i = 0
+ for interatom in interatomic_loop():
+ # No PCS.
+ if not hasattr(interatom, 'rdc'):
+ continue
+
+ # Check the loaded and back-calculated absolute values.
+ self.assertAlmostEqual(interatom.rdc['Gel'], T[i])
+ self.assertAlmostEqual(interatom.rdc_bc['Gel'], T_bc[i])
+
+ # Increment the spin index.
+ i += 1
+
+
def test_align_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
r20140 - in /branches/relax_disp: ./ pipe_control/ test_suite/ test_suite/shared_data/align_data/ test_suite/system_tests/ t...