Author: bugman
Date: Fri Nov 30 10:54:48 2012
New Revision: 18043
URL: http://svn.gna.org/viewcvs/relax?rev=18043&view=rev
Log:
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.
Added:
trunk/test_suite/shared_data/align_data/menthol/
trunk/test_suite/shared_data/align_data/menthol/long_range_rdc
trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
Modified:
trunk/test_suite/system_tests/n_state_model.py
Added: trunk/test_suite/shared_data/align_data/menthol/long_range_rdc
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/align_data/menthol/long_range_rdc?rev=18043&view=auto
==============================================================================
--- trunk/test_suite/shared_data/align_data/menthol/long_range_rdc (added)
+++ trunk/test_suite/shared_data/align_data/menthol/long_range_rdc Fri Nov 30
10:54:48 2012
@@ -1,0 +1,25 @@
+# Spin_ID1 Spin_ID2 RDC error Distance(angstroms)
+
+ @C4 @H13 -0.68 0.14 2.677771
+ @C5 @H13 0.95 0.14 2.129824
+ @C8 @H5 -0.50 0.28 2.834576
+ @C4 @H1 0.99 0.14 2.149821
+ @C10 @H13 -0.29 0.14 2.131881
+ @C9 @H13 -0.85 0.21 2.136622
+ @C1 @H1 0.40 0.21 3.460364
+ @C7 @H1 -0.59 0.14 2.765209
+ @C3 @H2 -1.01 0.14 2.143767
+ @C5 @H4 -0.26 0.14 3.488387
+ @C2 @H4 -0.25 0.14 2.162672
+ @C7 @H4 -0.47 0.14 2.767868
+ @C3 @Q7 1.94 0.14 2.772089
+ @C1 @Q7 3.85 0.14 3.487340
+ @C2 @H8 -0.54 0.14 3.474681
+ @C8 @H8 -1.18 0.28 2.779381
+ @C3 @H6 -0.39 0.28 2.709551
+ @C1 @H6 -0.70 0.14 2.730567
+ @C8 @H6 0.31 0.14 2.139753
+ @C7 @H4 -0.47 0.14 2.767868
+
+
+
Added: trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb?rev=18043&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb (added)
+++ trunk/test_suite/shared_data/structures/menthol_1R2S5R.pdb Fri Nov 30
10:54:48 2012
@@ -1,0 +1,63 @@
+HETATM 1 C1 UNK 1 1.425 -1.468 -0.176 1.00 0.00
C
+HETATM 2 C2 UNK 1 2.222 -0.280 0.360 1.00 0.00
C
+HETATM 3 C3 UNK 1 1.596 1.025 -0.136 1.00 0.00
C
+HETATM 4 C4 UNK 1 0.113 1.138 0.203 1.00 0.00
C
+HETATM 5 C5 UNK 1 -0.675 -0.055 -0.351 1.00 0.00
C
+HETATM 6 C6 UNK 1 -0.058 -1.354 0.183 1.00 0.00
C
+HETATM 7 H1 UNK 1 2.123 1.893 0.278 1.00 0.00
H
+HETATM 8 H2 UNK 1 2.150 -0.293 1.460 1.00 0.00
H
+HETATM 9 H3 UNK 1 1.538 -1.511 -1.270 1.00 0.00
H
+HETATM 10 H4 UNK 1 1.841 -2.404 0.218 1.00 0.00
H
+HETATM 11 H5 UNK 1 -0.003 1.177 1.293 1.00 0.00
H
+HETATM 12 H6 UNK 1 -0.527 -0.042 -1.447 1.00 0.00
H
+HETATM 13 H7 UNK 1 -0.160 -1.385 1.276 1.00 0.00
H
+HETATM 14 H8 UNK 1 -0.606 -2.221 -0.204 1.00 0.00
H
+HETATM 15 H9 UNK 1 1.708 1.077 -1.232 1.00 0.00
H
+HETATM 16 C7 UNK 1 3.698 -0.366 -0.023 1.00 0.00
C
+HETATM 17 H10 UNK 1 4.265 0.478 0.383 1.00 0.00
H
+HETATM 18 H11 UNK 1 4.151 -1.289 0.352 1.00 0.00
H
+HETATM 19 H12 UNK 1 3.813 -0.355 -1.112 1.00 0.00
H
+HETATM 20 C8 UNK 1 -2.192 0.066 -0.105 1.00 0.00
C
+HETATM 21 H13 UNK 1 -2.469 1.085 -0.399 1.00 0.00
H
+HETATM 22 C9 UNK 1 -2.586 -0.115 1.363 1.00 0.00
C
+HETATM 23 H14 UNK 1 -2.031 0.554 2.027 1.00 0.00
H
+HETATM 24 H15 UNK 1 -3.650 0.107 1.495 1.00 0.00
H
+HETATM 25 H16 UNK 1 -2.424 -1.143 1.700 1.00 0.00
H
+HETATM 26 C10 UNK 1 -2.981 -0.903 -0.989 1.00 0.00
C
+HETATM 27 H17 UNK 1 -4.057 -0.736 -0.878 1.00 0.00
H
+HETATM 28 H18 UNK 1 -2.730 -0.773 -2.046 1.00 0.00
H
+HETATM 29 H19 UNK 1 -2.786 -1.947 -0.722 1.00 0.00
H
+HETATM 30 O1 UNK 1 -0.416 2.389 -0.246 1.00 0.00
O
+HETATM 31 H20 UNK 1 -0.195 2.487 -1.181 1.00 0.00
H
+CONECT 1 2 6 9 10
+CONECT 26 20 27 28 29
+CONECT 2 1 3 8 16
+CONECT 3 2 4 7 15
+CONECT 4 3 5 11 30
+CONECT 5 4 6 12 20
+CONECT 6 1 5 13 14
+CONECT 16 2 17 18 19
+CONECT 20 5 21 22 26
+CONECT 22 20 23 24 25
+CONECT 7 3
+CONECT 17 16
+CONECT 18 16
+CONECT 19 16
+CONECT 21 20
+CONECT 23 22
+CONECT 24 22
+CONECT 25 22
+CONECT 27 26
+CONECT 28 26
+CONECT 29 26
+CONECT 8 2
+CONECT 31 30
+CONECT 9 1
+CONECT 10 1
+CONECT 11 4
+CONECT 12 5
+CONECT 13 6
+CONECT 14 6
+CONECT 15 3
+CONECT 30 4 31
+END
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=18043&r1=18042&r2=18043&view=diff
==============================================================================
--- trunk/test_suite/system_tests/n_state_model.py (original)
+++ trunk/test_suite/system_tests/n_state_model.py Fri Nov 30 10:54:48 2012
@@ -178,6 +178,22 @@
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, -0.351261/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayy, 0.556994/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axy, -0.506392/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Axz, 0.560544/2000)
+ self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.286367/2000)
+ self.assertAlmostEqual(cdp.chi2, 0.0)
+ self.assertAlmostEqual(cdp.q_rdc, 0.0)
+
+
def test_align_fit(self):
"""Test the use of RDCs and PCSs to find the alignment tensor."""
Added:
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py?rev=18043&view=auto
==============================================================================
---
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
(added)
+++
trunk/test_suite/system_tests/scripts/n_state_model/absolute_rdcs_menthol.py
Fri Nov 30 10:54:48 2012
@@ -1,0 +1,53 @@
+"""Script for testing the fitting of signless RDCs using menthol data."""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+
+# Path of the alignment data and structure.
+DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep+'menthol'
+STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+# Create the data pipe.
+self._execute_uf(uf_name='pipe.create', pipe_name='long-range RDC',
pipe_type='N-state')
+
+# Load the structure.
+self._execute_uf(uf_name='structure.read_pdb', file='menthol_1R2S5R.pdb',
dir=STRUCT_PATH)
+
+# Set up the 13C and 1H spins information.
+self._execute_uf(uf_name='structure.load_spins', spin_id='@C*',
ave_pos=False)
+self._execute_uf(uf_name='structure.load_spins', spin_id='@H*',
ave_pos=False)
+
+# Set up the pseudo-atoms.
+self._execute_uf(uf_name='spin.create_pseudo', spin_name='Q7',
members=['@H10', '@H11', '@H12'], averaging="linear")
+self._execute_uf(uf_name='spin.create_pseudo', spin_name='Q9',
members=['@H14', '@H15', '@H16'], averaging="linear")
+self._execute_uf(uf_name='spin.create_pseudo', spin_name='Q10',
members=['@H17', '@H18', '@H19'], averaging="linear")
+self._execute_uf(uf_name='sequence.display')
+
+# Define the nuclear isotopes of all spins and pseudo-spins.
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@Q*')
+
+# Load the RDC data.
+self._execute_uf(uf_name='rdc.read', align_id='Gel', file='long_range_rdc',
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
absolute=True)
+
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.read_dist', file='long_range_rdc',
dir=DATA_PATH, unit='Angstrom', spin_id1_col=1, spin_id2_col=2, data_col=5)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
+
+# Set up the model.
+self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
+
+# Minimisation.
+self._execute_uf(uf_name='minimise', min_algor='newton')
+
+# Show the tensors.
+self._execute_uf(uf_name='align_tensor.display')
+
+# Save the state.
+self._execute_uf(uf_name='state.save', file='devnull')
r18043 - in /trunk/test_suite: shared_data/align_data/menthol/ shared_data/structures/ system_tests/ system_tests/scripts/n_...