r11272 - /1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py -- July 02, 2010 - 10:40

Author: bugman
Date: Fri Jul  2 10:40:23 2010
New Revision: 11272

URL: http://svn.gna.org/viewcvs/relax?rev=11272&view=rev
Log:
Added a new system test for the direct optimisation of the paramagnetic 
centre.


Added:
    1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
      - copied, changed from r11271, 
1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py

Copied: 
1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py (from 
r11271, 1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py)
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py?p2=1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py&p1=1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py&r1=11271&r2=11272&rev=11272&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/align_fit.py (original)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py 
Fri Jul  2 10:40:23 2010
@@ -1,4 +1,4 @@
-"""Script for testing the fitting an alignment tensor to RDCs or PCSs."""
+"""Script for testing the fitting of the paramagnetic centre of the PCSs."""
 
 # Python module imports.
 import __main__
@@ -15,19 +15,15 @@
 STRUCT_PATH = __main__.install_path + 
sep+'test_suite'+sep+'shared_data'+sep+'structures'
 
 # Create the data pipe.
-pipe.create('rdc', 'N-state')
+pipe.create('para_centre', 'N-state')
 
 # Set the mode, if not specified by the system test.
 if not hasattr(ds, 'mode'):
     ds.mode = 'all'
 
 # The data to use.
-if hasattr(ds, 'rand') and ds.rand:
-    rdc_file = 'synth_rdc_rand'
-    pcs_file = 'synth_pcs_rand'
-else:
-    rdc_file = 'synth_rdc'
-    pcs_file = 'synth_pcs'
+rdc_file = 'synth_rdc'
+pcs_file = 'synth_pcs'
 
 # Load the CaM structure.
 structure.read_pdb(file='bax_C_1J7P_N_H_Ca', dir=STRUCT_PATH)
@@ -44,24 +40,23 @@
 value.set('1H', 'proton', spin_id="@N")
 
 # RDCs.
-if ds.mode in ['rdc', 'all']:
+if ds.mode == 'all':
     rdc.read(align_id='synth', file=rdc_file, 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)
 
 # PCSs.
-if ds.mode in ['pcs', 'all']:
-    pcs.read(align_id='synth', file=pcs_file, 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)
+pcs.read(align_id='synth', file=pcs_file, 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)
 
-    # Set the paramagnetic centre.
-    pcs.centre(atom_id=':1000@CA')
+# The temperature.
+temperature(id='synth', temp=303)
 
-    # The temperature.
-    temperature(id='synth', temp=303)
-
-    # The frequency.
-    frq.set(id='synth', frq=600.0 * 1e6)
+# The frequency.
+frq.set(id='synth', frq=600.0 * 1e6)
 
 # Set up the model.
 n_state_model.select_model(model='fixed')
+
+# Paramagnetic centre optimisation.
+n_state_model.fix_paramag_centre(fix=False)
 
 # Set the tensor elements.
 #cdp.align_tensors[0].Axx = -0.351261/2000