r16857 - /branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py -- June 11, 2012 - 20:23

Author: bugman
Date: Mon Jun 11 20:23:02 2012
New Revision: 16857

URL: http://svn.gna.org/viewcvs/relax?rev=16857&view=rev
Log:
Added the script for the system test of the last commit (r16856).


Added:
    
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py

Added: 
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py?rev=16857&view=auto
==============================================================================
--- 
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
 (added)
+++ 
branches/absolute_rdc/test_suite/system_tests/scripts/n_state_model/absolute_rdcs.py
 Mon Jun 11 20:23:02 2012
@@ -1,0 +1,50 @@
+"""Script for testing the fitting of signless RDCs."""
+
+# 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+'CaM'
+STRUCT_PATH = status.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+# Create a data pipe.
+self._execute_uf(uf_name='pipe.create', pipe_name='abs', pipe_type='N-state')
+
+# Load the CaM structure.
+self._execute_uf(uf_name='structure.read_pdb', file='bax_C_1J7P_N_H_Ca', 
dir=STRUCT_PATH)
+
+# Load the spins.
+self._execute_uf(uf_name='structure.load_spins')
+
+# Load the NH vectors.
+self._execute_uf(uf_name='structure.vectors', spin_id='@N', attached='H', 
ave=False)
+
+# Set the values needed to calculate the dipolar constant.
+self._execute_uf(1.041 * 1e-10, 'r', spin_id="@N", uf_name='value.set')
+self._execute_uf('15N', 'heteronuc_type', spin_id="@N", uf_name='value.set')
+self._execute_uf('1H', 'proton_type', spin_id="@N", uf_name='value.set')
+
+# Load the RDCs (both a signed and absolute value version).
+self._execute_uf(uf_name='rdc.read', align_id='signed', file='synth_rdc', 
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, 
spin_name_col=5, data_col=6)
+#self._execute_uf(uf_name='rdc.read', align_id='abs', file='synth_rdc_abs', 
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, 
spin_name_col=5, data_col=6, absolute=True)
+
+# Set up the model.
+self._execute_uf(uf_name='n_state_model.select_model', model='fixed')
+
+# Minimisation.
+self._execute_uf(uf_name='grid_search', inc=3)
+self._execute_uf('simplex', constraints=False, max_iter=500, 
uf_name='minimise')
+
+# Write out a results file.
+self._execute_uf('devnull', force=True, uf_name='results.write')
+
+# Show the tensors.
+self._execute_uf(uf_name='align_tensor.display')
+
+# Print the contents of the current data pipe (for debugging Q-values).
+print(cdp)
+print((cdp.align_tensors[0]))