Author: bugman
Date: Thu Oct 6 14:52:44 2011
New Revision: 14806
URL: http://svn.gna.org/viewcvs/relax?rev=14806&view=rev
Log:
Created the N-state model test_rdc_tensor() system test for catching a
strange RDC back calc bug.
Added:
1.3/test_suite/shared_data/align_data/CaM/rdc_dy
1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
Modified:
1.3/test_suite/system_tests/n_state_model.py
Added: 1.3/test_suite/shared_data/align_data/CaM/rdc_dy
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/shared_data/align_data/CaM/rdc_dy?rev=14806&view=auto
==============================================================================
--- 1.3/test_suite/shared_data/align_data/CaM/rdc_dy (added)
+++ 1.3/test_suite/shared_data/align_data/CaM/rdc_dy Thu Oct 6 14:52:44 2011
@@ -1,0 +1,16 @@
+# res_num spin_name rdc error
+ 4 N -6.41 1.0
+ 5 N -21.55 1.0
+ 7 N 8.25 1.0
+ 12 N -9.12 1.0
+ 33 N -30.02 1.0
+ 35 N -37.07 1.0
+ 45 N 3.33 1.0
+ 46 N -2.04 1.0
+ 79 N -2.33 1.0
+ 80 N -3.61 1.0
+ 82 N -5.77 1.0
+ 87 N -32.93 1.0
+ 88 N -13.49 1.0
+ 96 N 12.33 1.0
+ 101 N 21.21 1.0
Modified: 1.3/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/n_state_model.py?rev=14806&r1=14805&r2=14806&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/n_state_model.py (original)
+++ 1.3/test_suite/system_tests/n_state_model.py Thu Oct 6 14:52:44 2011
@@ -480,6 +480,13 @@
self.assertAlmostEqual(cdp.mol[0].res[2].spin[0].rdc_bc['A'],
-16.244078605100817)
+ def test_rdc_tensor(self):
+ """Test the calculation of an alignment tensor from RDC data."""
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'rdc_tensor.py')
+
+
def test_stereochem_analysis(self):
"""The full relative stereochemistry analysis."""
Added: 1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py?rev=14806&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py (added)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py Thu Oct
6 14:52:44 2011
@@ -1,0 +1,64 @@
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from physical_constants import NH_BOND_LENGTH_RDC
+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+'CaM'
+STRUCT_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+# The tag.
+tag = "Dy C-dom"
+
+# Create the data pipe.
+pipe.create(tag, 'N-state')
+
+# Load the CaM structures.
+structure.read_pdb('bax_C_1J7P_N_H_Ca.pdb', dir=STRUCT_PATH)
+
+# Load the spins.
+structure.load_spins('@N', ave_pos=False)
+structure.load_spins('@H', ave_pos=False)
+
+# Load the NH vectors.
+structure.vectors('H', '@N', ave=False)
+
+# Set the values needed to calculate the dipolar constant.
+value.set(NH_BOND_LENGTH_RDC, 'bond_length')
+value.set('15N', 'heteronucleus')
+value.set('1H', 'proton')
+
+# RDCs.
+rdc.read(tag, file='rdc_dy', dir=DATA_PATH, res_num_col=1, spin_name_col=2,
data_col=3, error_col=4, neg_g_corr=True)
+
+# Set up the model.
+n_state_model.select_model('fixed')
+
+# Minimisation.
+grid_search(inc=3)
+minimise('newton', constraints=False)
+
+# Monte Carlo simulations.
+monte_carlo.setup(number=3)
+monte_carlo.create_data()
+monte_carlo.initial_values()
+minimise('newton', constraints=False)
+monte_carlo.error_analysis()
+
+# Show the tensors.
+align_tensor.display(tag)
+
+# Back calc.
+rdc.back_calc()
+
+# Q-factors.
+rdc.calc_q_factors()
+
+# Correlation plots.
+rdc.corr_plot(file="%s_rdc_corr.agr" % 'C', force=True)
+
+# Save the program state.
+state.save('relax_tensors', force=True)
r14806 - in /1.3/test_suite: shared_data/align_data/CaM/ system_tests/ system_tests/scripts/n_state_model/