r16919 - /branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py -- June 17, 2012 - 10:25

Author: bugman
Date: Sun Jun 17 10:25:20 2012
New Revision: 16919

URL: http://svn.gna.org/viewcvs/relax?rev=16919&view=rev
Log:
Redesigned the model-free dauvergne_protocol.py system test script for the 
interatomic concept.

The new script will be used to redesign how to set up a model-free analysis 
using the interatomic
data concept.  It adds the new relax_data.dipole_pair user function which 
will be used to define the
dipolar relaxation interaction (this will inadvertently allow multi-dipole 
relation).  The
heteronuc_type and proton_type parameters have been replaced with the 
spin_type parameter, as now
both the heternuclear and homonuclear spins need to be loaded into relax.


Modified:
    
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py

Modified: 
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py?rev=16919&r1=16918&r2=16919&view=diff
==============================================================================
--- 
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
 (original)
+++ 
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
 Sun Jun 17 10:25:20 2012
@@ -186,15 +186,12 @@
 # The data path.
 data_path = status.install_path + sep + 'test_suite' + sep + 'shared_data' + 
sep + 'model_free' + sep + 'sphere' + sep
 
-# Load the sequence.
-sequence.read(file='noe.500.out', dir=data_path, mol_name_col=1, 
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5)
-
-# Name the spins.
-spin.name(name='N')
-
 # Load the PDB file.
 structure.read_pdb('sphere.pdb', dir=data_path)
-structure.vectors(attached='H')
+
+# Load all the N and H spins.
+structure.load_spins('@N', ave_pos=True)
+structure.load_spins('@H', ave_pos=True)
 
 # Load the relaxation data.
 relax_data.read(ri_id='R1_900',  ri_type='R1',  frq=900*1e6, 
file='r1.900.out',  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, error_col=7)
@@ -204,11 +201,16 @@
 relax_data.read(ri_id='R2_500',  ri_type='R2',  frq=500*1e6, 
file='r2.500.out',  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, error_col=7)
 relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500*1e6, 
file='noe.500.out', 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, error_col=7)
 
-# Set the bond length, CSA values, heteronucleus type, and proton type.
+# Define the dipolar relaxation interaction.
+relax_data.dipole_pair(spin_id1='@N', spin_id2='@H', direct_bond=True)
 value.set(1.02 * 1e-10, 'r')
+
+# Define the CSA relaxation interaction.
 value.set(-172 * 1e-6, 'csa')
-value.set('15N', 'heteronuc_type')
-value.set('1H', 'proton_type')
+
+# Set the spin types.
+value.set('15N', 'spin_type', spin_id='@N')
+value.set('1H', 'spin_type', spin_id='@H')