Author: bugman
Date: Fri Nov 30 13:01:39 2012
New Revision: 18049
URL: http://svn.gna.org/viewcvs/relax?rev=18049&view=rev
Log:
Merged revisions 18043-18048 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18043 | bugman | 2012-11-30 10:54:48 +0100 (Fri, 30 Nov 2012) | 5 lines
Created the N_state_model.test_absolute_rdc_menthol system test to
demonstrate a pseudo-atom failure.
This is a test of the long range, absolute RDCs for menthol.
........
r18044 | bugman | 2012-11-30 10:58:01 +0100 (Fri, 30 Nov 2012) | 7 lines
Bug fix for the use of pseudo-atoms for RDCs in the N-state model analysis.
If the second atom of the pair in the intermolecular data container holding
the RDC data was a
pseudo-atom, then the N-state model optimisation setup would fail. Now
both the first and second
atoms being pseudo-atoms is supported.
........
r18045 | bugman | 2012-11-30 11:03:20 +0100 (Fri, 30 Nov 2012) | 3 lines
Fixes for the N_state_model.test_absolute_rdc_menthol system test checks to
match the data.
........
r18046 | bugman | 2012-11-30 11:17:02 +0100 (Fri, 30 Nov 2012) | 3 lines
Added a check for the second Q factor in the
N_state_model.test_absolute_rdc_menthol system test.
........
r18047 | bugman | 2012-11-30 12:57:10 +0100 (Fri, 30 Nov 2012) | 6 lines
Modified the N_state_model.test_populations system test to catch bug #20335.
This simply adds calls to the rdc.delete and pcs.delete user functions, and
then reloads the RDC and
PCS data.
........
r18048 | bugman | 2012-11-30 13:00:20 +0100 (Fri, 30 Nov 2012) | 5 lines
Fix for bug #20335 (https://gna.org/bugs/?20335).
The global alignment ID data structure now has the RDC or PCS ID string
correctly removed.
........
Added:
branches/frame_order_testing/test_suite/shared_data/align_data/menthol/
- copied from r18048, trunk/test_suite/shared_data/align_data/menthol/
branches/frame_order_testing/test_suite/shared_data/structures/menthol_1R2S5R.pdb
- copied unchanged from r18048,
trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
- copied unchanged from r18048,
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/pcs.py
branches/frame_order_testing/generic_fns/rdc.py
branches/frame_order_testing/specific_fns/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/n_state_model.py
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Nov 30 13:01:39 2012
@@ -1,1 +1,1 @@
-/trunk:1-18032
+/trunk:1-18048
Modified: branches/frame_order_testing/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pcs.py?rev=18049&r1=18048&r2=18049&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/pcs.py (original)
+++ branches/frame_order_testing/generic_fns/pcs.py Fri Nov 30 13:01:39 2012
@@ -448,7 +448,7 @@
# Clean the global data.
if not hasattr(cdp, 'rdc_ids') or id not in cdp.rdc_ids:
- cdp.align_ids.pop(id)
+ cdp.align_ids.pop(cdp.align_ids.index(id))
def display(align_id=None, bc=False):
Modified: branches/frame_order_testing/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/rdc.py?rev=18049&r1=18048&r2=18049&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/rdc.py (original)
+++ branches/frame_order_testing/generic_fns/rdc.py Fri Nov 30 13:01:39 2012
@@ -371,7 +371,7 @@
# Clean the global data.
if not hasattr(cdp, 'pcs_ids') or id not in cdp.pcs_ids:
- cdp.align_ids.pop(id)
+ cdp.align_ids.pop(cdp.align_ids.index(id))
def display(align_id=None, bc=False):
Modified: branches/frame_order_testing/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/n_state_model.py?rev=18049&r1=18048&r2=18049&view=diff
==============================================================================
--- branches/frame_order_testing/specific_fns/n_state_model.py (original)
+++ branches/frame_order_testing/specific_fns/n_state_model.py Fri Nov 30
13:01:39 2012
@@ -1092,7 +1092,7 @@
# Pseudo-atom set up.
if (hasattr(spin1, 'members') or hasattr(spin2, 'members'))
and align_id in interatom.rdc.keys():
# Skip non-Me groups.
- if len(spin1.members) != 3:
+ if (hasattr(spin1, 'members') and len(spin1.members) !=
3) or (hasattr(spin2, 'members') and len(spin2.members) != 3):
continue
# The RDC for the Me-pseudo spin where:
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=18049&r1=18048&r2=18049&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 Fri
Nov 30 13:01:39 2012
@@ -178,6 +178,23 @@
i += 1
+ def test_absolute_rdc_menthol(self):
+ """Test the fitting of signless RDCs for menthol."""
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'absolute_rdcs_menthol.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -9.784232367053e-05)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, -7.158933725824e-05)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, 4.467570786770e-06)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 5.153319781627e-06)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, 1.801211682780e-04)
+ self.assertAlmostEqual(cdp.chi2, 1044.9572886805781)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+ self.assertAlmostEqual(cdp.q_rdc_norm2, 0.81262759306400001)
+
+
def test_align_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py?rev=18049&r1=18048&r2=18049&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/n_state_model/populations.py
Fri Nov 30 13:01:39 2012
@@ -59,6 +59,25 @@
# The frequency.
self._execute_uf(uf_name='frq.set', id=align_list[i], frq=799.75376122 *
1e6)
+# Try to delete the RDC and PCS data (bug #20335,
https://gna.org/bugs/?20335).
+self._execute_uf(uf_name='pcs.delete')
+self._execute_uf(uf_name='rdc.delete')
+
+# Load the RDCs and PCSs.
+for i in range(len(align_list)):
+ # The RDC (skip the list at index 1, as this has zero data and now
causes a RelaxError).
+ if i != 1:
+ self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='missing_rdc_%i' % i, dir=data_path, spin_id1_col=1, spin_id2_col=2,
data_col=3, error_col=None)
+
+ # The PCS.
+ self._execute_uf(uf_name='pcs.read', align_id=align_list[i],
file='missing_pcs_%i' % i, dir=data_path, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=5, data_col=6,
error_col=None)
+
+ # The temperature.
+ self._execute_uf(uf_name='temperature', id=align_list[i], temp=298)
+
+ # 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])
r18049 - in /branches/frame_order_testing: ./ generic_fns/ specific_fns/ test_suite/shared_data/align_data/menthol/ test_sui...