r17168 - in /branches/interatomic/test_suite/system_tests: palmer.py scripts/palmer.py -- July 03, 2012 - 22:14

Author: bugman
Date: Tue Jul  3 22:14:59 2012
New Revision: 17168

URL: http://svn.gna.org/viewcvs/relax?rev=17168&view=rev
Log:
Converted the Palmer.test_palmer() system test to the interatomic data design.


Modified:
    branches/interatomic/test_suite/system_tests/palmer.py
    branches/interatomic/test_suite/system_tests/scripts/palmer.py

Modified: branches/interatomic/test_suite/system_tests/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/palmer.py?rev=17168&r1=17167&r2=17168&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/palmer.py (original)
+++ branches/interatomic/test_suite/system_tests/palmer.py Tue Jul  3 
22:14:59 2012
@@ -59,7 +59,7 @@
         self.script_exec(status.install_path + 
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'palmer.py')
 
         # Determine if the Gnu gcc or Portland C compiler version is being 
used.
-        spin = return_spin(':0', pipe='m2')
+        spin = return_spin(':0@N', pipe='m2')
         if spin.te == 1.951*1e-12:
             compiler = 'gcc'    # Gnu gcc modelfree4 version.
         else:
@@ -68,7 +68,7 @@
         # Checks for model m1, m2, and m3 mfout file reading.
         models = ['m1', 'm2', 'm3']
         params = [['s2'], ['s2', 'te'], ['s2', 'rex']]
-        spin_names = [':-2&:Gly', ':-1&:Gly', ':0&:Gly']
+        spin_names = [':-2@N', ':-1@N', ':0@N']
         if compiler == 'gcc':
             s2 = [[0.869, 0.732, None], [0.869, 0.730, None], [0.715, 0.643, 
None]]
             te = [[None, None, None], [0.0, 1.951, None], [None, None, 
None]]    # Gnu gcc modelfree4 version.
@@ -182,9 +182,6 @@
         chi2 = [[143.6773, 105.1767, 61.6684], [40.9055, 57.1562, 48.4927], 
[143.6773, 105.1767, 61.6684]]
 
         # Checks for model m1, m2, and m3 mfout file reading.
-        print ds['m1'].mol[0].res
-        print ds['m1'].mol[0].res[0]
-        print ds['m1'].mol[0].res[0].spin
         for model_index in xrange(3):
             print(("Model " + repr(models[model_index])))
             for spin_index in xrange(3):

Modified: branches/interatomic/test_suite/system_tests/scripts/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/palmer.py?rev=17168&r1=17167&r2=17168&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/palmer.py (original)
+++ branches/interatomic/test_suite/system_tests/scripts/palmer.py Tue Jul  3 
22:14:59 2012
@@ -34,11 +34,25 @@
         relax_data.read(ri_id='R2_600',  ri_type='R2',  frq=600.0*1e6, 
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R2.dat',
 res_num_col=1, res_name_col=2, data_col=3, error_col=4)
         relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6, 
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
 res_num_col=1, res_name_col=2, data_col=3, error_col=4)
 
+        # Name the spins, then attach some protons.
+        spin.name('N')
+        sequence.attach_protons()
+
         # Setup other values.
         diffusion_tensor.init(1e-8)
-        value.set('15N', 'heteronuc_type')
-        value.set(1.02 * 1e-10, 'r')
-        value.set(-172 * 1e-6, 'csa')
+
+        # Define the magnetic dipole-dipole relaxation interaction.
+        spin.element(element='N', spin_id='@N')
+        spin.element(element='H', spin_id='@H')
+        dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+        dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 
1e-10)
+
+        # Define the chemical shift relaxation interaction.
+        value.set(-172 * 1e-6, 'csa', spin_id='@N')
+        
+        # Set the nuclear isotope type.
+        spin.isotope('15N', spin_id='@N')
+        spin.isotope('1H', spin_id='@H')
 
         # Select the model-free model.
         model_free.select_model(model=name)