r8796 - /1.3/test_suite/system_tests/scripts/align_fit.py -- February 12, 2009 - 20:08

Author: bugman
Date: Thu Feb 12 20:08:38 2009
New Revision: 8796

URL: http://svn.gna.org/viewcvs/relax?rev=8796&view=rev
Log:
Modified the system test script to allow different combinations of RDC and/or 
PCS loading.


Modified:
    1.3/test_suite/system_tests/scripts/align_fit.py

Modified: 1.3/test_suite/system_tests/scripts/align_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/align_fit.py?rev=8796&r1=8795&r2=8796&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/align_fit.py (original)
+++ 1.3/test_suite/system_tests/scripts/align_fit.py Thu Feb 12 20:08:38 2009
@@ -15,6 +15,10 @@
 pipe.create('rdc', 'N-state')
 cdp = pipes.get_pipe()
 
+# Set the mode, if not specified by the system test.
+if not hasattr(cdp, 'mode'):
+    cdp.mode = 'all'
+
 # Load the CaM structure.
 structure.read_pdb(file='bax_C_1J7P_N_H_Ca', dir=STRUCT_PATH)
 
@@ -22,42 +26,46 @@
 structure.load_spins()
 
 # Load the NH vectors.
-structure.vectors(spin_id='@N', attached='H')
+structure.vectors(spin_id='@N', attached='H', ave=False)
 
 # Set the values needed to calculate the dipolar constant.
 value.set(1.02 * 1e-10, 'bond_length', spin_id="@N")
 value.set('15N', 'heteronucleus', spin_id="@N")
 value.set('1H', 'proton', spin_id="@N")
 
-# Load the RDCs and PCSs.
-rdc.read(id='synth', file='synth_rdc', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5)
-pcs.read(id='synth', file='synth_pcs', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5)
+# RDCs.
+if cdp.mode in ['rdc', 'all']:
+    rdc.read(id='synth', file='synth_rdc', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5)
 
-# Set the paramagnetic centre.
-pcs.centre(atom_id=':1001@CA')
+# PCSs.
+if cdp.mode in ['pcs', 'all']:
+    pcs.read(id='synth', file='synth_pcs', dir=DATA_PATH, mol_name_col=0, 
res_num_col=1, res_name_col=2, spin_num_col=3, spin_name_col=4, data_col=5)
 
-# The temperature.
-temperature(id='synth', temp=303)
+    # Set the paramagnetic centre.
+    pcs.centre(atom_id=':1001@CA')
 
-# The frequency.
-frq.set(id='synth', frq=600.0 * 1e6)
+    # The temperature.
+    temperature(id='synth', temp=303)
+
+    # The frequency.
+    frq.set(id='synth', frq=600.0 * 1e6)
 
 # Set up the model.
 n_state_model.select_model(model='fixed')
 
 # Set the tensor elements.
-cdp.align_tensors[0].Axx = -0.351261/2000
-cdp.align_tensors[0].Ayy = 0.556994/2000
-cdp.align_tensors[0].Axy = -0.506392/2000
-cdp.align_tensors[0].Axz = 0.560544/2000
-cdp.align_tensors[0].Ayz = -0.286367/2000
+#cdp.align_tensors[0].Axx = -0.351261/2000
+#cdp.align_tensors[0].Ayy = 0.556994/2000
+#cdp.align_tensors[0].Axy = -0.506392/2000
+#cdp.align_tensors[0].Axz = 0.560544/2000
+#cdp.align_tensors[0].Ayz = -0.286367/2000
 
 # Minimisation.
-#grid_search(inc=5)
+grid_search(inc=3)
 minimise('simplex', constraints=False, max_iter=500)
 
 # Write out a results file.
-results.write('results', force=True)
+results.write('devnull', force=True)
 
 # Show the tensors.
 align_tensor.display()