Author: bugman
Date: Wed Nov 13 22:06:46 2013
New Revision: 21436
URL: http://svn.gna.org/viewcvs/relax?rev=21436&view=rev
Log:
Created the N_state_model.test_pyrotartaric_anhydride_mix system test.
This is used to demonstrate a bug in the N-state analysis using mixed RDC and
long range absolute
J+D data.
Added:
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range
- copied, changed from r21435,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range
- copied, changed from r21435,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs
Modified:
trunk/test_suite/system_tests/n_state_model.py
trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
Copied:
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range
(from r21435,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range?p2=trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range&p1=trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs&r1=21435&r2=21436&rev=21436&view=diff
==============================================================================
--- trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs
(original)
+++
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_long_range
Wed Nov 13 22:06:46 2013
@@ -1,14 +1,4 @@
#spin_id1 spin_id2 RDC abs(T)
abs(J) J_sign dist
-#@9 @10 22.76303880266 147.25303880266
124.49000000000 1 1.089841
-#@9 @11 -14.90302123027 108.71697876973
123.62000000000 1 1.090724
-#@9 @12 13.29511331547 135.81511331547
122.52000000000 1 1.091948
-@9 @10 1 1 1
1 1.089841
-@9 @11 1 1 1
1 1.090724
-@9 @12 1 1 1
1 1.091948
-@9 @Q9 7.051710295953332 130.59171029595333
123.54000000000 1 1.090837
-@4 @6 14.64956993990 141.23956993990
126.59000000000 1 1.095136
-@5 @7 -9.80224941614 117.98775058386
127.79000000000 1 1.093495
-@5 @8 4.49085022708 138.87085022708
134.38000000000 1 1.088982
@1 @6 1.16041049951 2.16041049951
1.00000000000 1 2.996136
@3 @6 0.57071216172 6.81928783828
7.39000000000 -1 2.091217
@5 @6 3.68667449742 0.46667449742
3.22000000000 -1 2.163545
Copied:
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range
(from r21435,
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range?p2=trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range&p1=trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs&r1=21435&r2=21436&rev=21436&view=diff
==============================================================================
--- trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs
(original)
+++
trunk/test_suite/shared_data/align_data/pyrotartaric_anhydride/R_rdcs_short_range
Wed Nov 13 22:06:46 2013
@@ -9,36 +9,3 @@
@4 @6 14.64956993990 141.23956993990
126.59000000000 1 1.095136
@5 @7 -9.80224941614 117.98775058386
127.79000000000 1 1.093495
@5 @8 4.49085022708 138.87085022708
134.38000000000 1 1.088982
-@1 @6 1.16041049951 2.16041049951
1.00000000000 1 2.996136
-@3 @6 0.57071216172 6.81928783828
7.39000000000 -1 2.091217
-@5 @6 3.68667449742 0.46667449742
3.22000000000 -1 2.163545
-@9 @6 -2.26063357144 7.18063357144
4.92000000000 -1 2.150225
-@1 @7 -4.77232431456 11.97232431456
7.20000000000 -1 2.114901
-@3 @7 -0.17007443173 0.55992556827
0.73000000000 1 3.043440
-@4 @7 2.37501105989 0.82498894011
3.20000000000 -1 2.192949
-@9 @7 1.64523216045 7.67523216045
6.03000000000 1 2.673710
-@1 @8 -0.94447557779 6.19447557779
5.25000000000 -1 2.139021
-@3 @8 0.06213688971 6.42213688971
6.36000000000 1 3.252832
-@4 @8 1.48958862680 0.14958862680
1.34000000000 -1 2.219687
-@9 @8 0.21349779284 1.16349779284
0.95000000000 1 3.256413
-@3 @Q9 -1.2400897128766667 4.472910287123334
5.71300000000 1 9999.0
-@4 @Q9 -1.8997427023766667 5.669742702376667
3.77000000000 -1 9999.0
-@5 @Q9 -0.0129325208733333 4.917067479126667
4.93000000000 1 9999.0
-#@3 @10 -0.89720954952 1.16279045048
2.06000000000 1 2.778083
-#@4 @10 0.40534850610 3.44465149390
3.85000000000 -1 2.168145
-#@5 @10 0.45779735990 10.76779735990
10.31000000000 1 3.527661
-#@3 @11 -0.87177225738 11.85822774262
12.73000000000 1 3.473732
-#@4 @11 -3.87776069286 7.43776069286
3.56000000000 -1 2.159521
-#@5 @11 -0.20558867187 1.19441132813
1.40000000000 1 2.888372
-#@3 @12 -1.95128733173 0.39871266827
2.35000000000 1 2.826109
-#@4 @12 -2.22681592037 6.12681592037
3.90000000000 -1 2.173800
-#@5 @12 -0.29100625065 2.78899374935
3.08000000000 1 2.849230
-@3 @10 1 1 1
1 2.778083
-@4 @10 1 1 1
1 2.168145
-@5 @10 1 1 1
1 3.527661
-@3 @11 1 1 1
1 3.473732
-@4 @11 1 1 1
1 2.159521
-@5 @11 1 1 1
1 2.888372
-@3 @12 1 1 1
1 2.826109
-@4 @12 1 1 1
1 2.173800
-@5 @12 1 1 1
1 2.849230
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=21436&r1=21435&r2=21436&view=diff
==============================================================================
--- trunk/test_suite/system_tests/n_state_model.py (original)
+++ trunk/test_suite/system_tests/n_state_model.py Wed Nov 13 22:06:46 2013
@@ -920,11 +920,11 @@
self.assertAlmostEqual(cdp.interatomic[2].rdc_bc['A'],
-16.244078605100817)
- def test_pyrotartaric_anhydride_rdcs(self):
- """Pyrotarctic anhydride alignment tensor optimisation using long
range (1J, 2J & 3J) RDC data."""
+ def test_pyrotartaric_anhydride_absT(self):
+ """Pyrotarctic anhydride alignment tensor optimisation using long
range (1J, 2J & 3J) absolute T (J+D) data."""
# The setup.
- ds.abs_data = False
+ ds.abs_data = 'T'
# Execute the script.
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'pyrotartaric_anhydride.py')
@@ -939,11 +939,30 @@
self.assertAlmostEqual(cdp.q_rdc, 0.0, 2)
- def test_pyrotartaric_anhydride_absT(self):
- """Pyrotarctic anhydride alignment tensor optimisation using long
range (1J, 2J & 3J) absolute T (J+D) data."""
+ def test_pyrotartaric_anhydride_mix(self):
+ """Pyrotarctic anhydride alignment tensor optimisation using short
range RDC and long range (1J, 2J & 3J) absolute T (J+D) data."""
# The setup.
- ds.abs_data = True
+ ds.abs_data = 'mix'
+
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'pyrotartaric_anhydride.py')
+
+ # Test the optimised values.
+ self.assertAlmostEqual(cdp.align_tensors[0].Axx, -0.0001756305, 5)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.000278497, 5)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.000253196, 5)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.000280272, 5)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.0001431835, 5)
+ self.assertAlmostEqual(cdp.chi2, 0.0, 2)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0, 2)
+
+
+ def test_pyrotartaric_anhydride_rdcs(self):
+ """Pyrotarctic anhydride alignment tensor optimisation using long
range (1J, 2J & 3J) RDC data."""
+
+ # The setup.
+ ds.abs_data = 'D'
# Execute the script.
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'pyrotartaric_anhydride.py')
Modified:
trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py?rev=21436&r1=21435&r2=21436&view=diff
==============================================================================
---
trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
(original)
+++
trunk/test_suite/system_tests/scripts/n_state_model/pyrotartaric_anhydride.py
Wed Nov 13 22:06:46 2013
@@ -13,7 +13,7 @@
# Setup for stand-alone operation.
if not hasattr(ds, 'abs_data'):
- ds.abs_data = True
+ ds.abs_data = 'mix'
# Path of the files.
str_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
@@ -42,13 +42,22 @@
self._execute_uf(uf_name='interatom.read_dist', file='R_rdcs',
dir=data_path, unit='Angstrom', spin_id1_col=1, spin_id2_col=2, data_col=7)
self._execute_uf(uf_name='interatom.unit_vectors', ave=False)
+# Load the short range RDC data and long range J and J+D data.
+if ds.abs_data == 'mix':
+ # Short range RDCs.
+ self._execute_uf(uf_name='rdc.read', align_id='test',
file='R_rdcs_short_range', dir=data_path, data_type='D', spin_id1_col=1,
spin_id2_col=2, data_col=4, absolute=False)
+
+ # Long range J and J+D data.
+ self._execute_uf(uf_name='rdc.read', align_id='test',
file='R_rdcs_long_range', dir=data_path, data_type='T', spin_id1_col=1,
spin_id2_col=2, data_col=4, absolute=True)
+ self._execute_uf(uf_name='j_coupling.read', file='R_rdcs_long_range',
dir=data_path, spin_id1_col=1, spin_id2_col=2, data_col=5, sign_col=6)
+
# Load the J and J+D data.
-if ds.abs_data:
+elif ds.abs_data == 'T':
self._execute_uf(uf_name='rdc.read', align_id='test', file='R_rdcs',
dir=data_path, data_type='T', spin_id1_col=1, spin_id2_col=2, data_col=4,
absolute=True)
self._execute_uf(uf_name='j_coupling.read', file='R_rdcs',
dir=data_path, spin_id1_col=1, spin_id2_col=2, data_col=5, sign_col=6)
# Load the RDC data.
-else:
+elif ds.abs_data == 'D':
self._execute_uf(uf_name='rdc.read', align_id='test', file='R_rdcs',
dir=data_path, spin_id1_col=1, spin_id2_col=2, data_col=3)
# Set up the model.
r21436 - in /trunk/test_suite: shared_data/align_data/pyrotartaric_anhydride/ system_tests/ system_tests/scripts/n_state_model/