r16925 - in /branches/interatomic: test_suite/system_tests/scripts/model_free/ user_functions/ -- June 17, 2012 - 23:22

Author: bugman
Date: Sun Jun 17 23:22:09 2012
New Revision: 16925

URL: http://svn.gna.org/viewcvs/relax?rev=16925&view=rev
Log:
A few changes to the relax_data.dipole_pair user function definition.


Modified:
    
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
    branches/interatomic/user_functions/relax_data.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=16925&r1=16924&r2=16925&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 23:22:09 2012
@@ -202,7 +202,8 @@
 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)
 
 # Define the magnetic dipole-dipole relaxation interaction.
-relax_data.dipole_pair(spin_id1='@N', spin_id2='@H', dist=1.02 * 1e-10, 
direct_bond=True)
+relax_data.dipole_pair(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10, 
direct_bond=True)
+vectors(spin_id1='@N', spin_id2='@H', direct_bond=True)
 
 # Define the chemical shift relaxation interaction.
 value.set(-172 * 1e-6, 'csa')

Modified: branches/interatomic/user_functions/relax_data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/relax_data.py?rev=16925&r1=16924&r2=16925&view=diff
==============================================================================
--- branches/interatomic/user_functions/relax_data.py (original)
+++ branches/interatomic/user_functions/relax_data.py Sun Jun 17 23:22:09 2012
@@ -181,10 +181,10 @@
     desc = "The spin identification string for the second spin of the 
dipolar relaxation pair."
 )
 uf.add_keyarg(
-    name = "dist",
+    name = "ave_dist",
     default = NH_BOND_LENGTH,
     py_type = "float",
-    desc_short = "interatomic distance (meters)",
+    desc_short = "averaged interatomic distance (meters)",
     desc = "The r^-3 averaged distance between the two spins to be used in 
the magnetic dipole constant."
 )
 uf.add_keyarg(
@@ -198,17 +198,17 @@
 uf.desc.append(Desc_container())
 uf.desc[-1].add_paragraph("To analyse relaxation data, the relaxation 
mechanism and related parameters needs to be defined.  This user function 
allows pairs of spins which are coupled via the magnetic dipole-dipole 
interaction to be defined.  Hence the dipolar relaxation mechanism between 
the two spins is to be considered active.")
 uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as 
model-free analysis with the spheroidal and ellipsoidal global diffusion 
tensors, the two spins should already possess positional information.  This 
information will be used by this user function to calculate unit vectors 
between the two spins.  Without positional information, no vectors can be 
calculated and an orientational dependent analysis will not be possible.")
-uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is 
averaged in NMR over the interatomic distance to the inverse third power, the 
interatomic distances within a 3D structural file are of no use for defining 
the interaction.  Therefore these distances must be explicitly defined.")
+uf.desc[-1].add_paragraph("As the magnetic dipole-dipole interaction is 
averaged in NMR over the interatomic distance to the inverse third power, the 
interatomic distances within a 3D structural file are of no use for defining 
the interaction.  Therefore these average distances must be explicitly 
defined.")
 # Prompt examples.
 uf.desc.append(Desc_container("Prompt examples"))
 uf.desc[-1].add_paragraph("To set up the protein 15N heteronuclear 
relaxation mechanism, type on of the following:")
 uf.desc[-1].add_prompt("relax> relax_data.dipole_pair('@N', '@H', 1.02 * 
1e-10, True)")
-uf.desc[-1].add_prompt("relax> relax_data.dipole_pair(spin_id1='@N', 
spin_id2='@H', dist=1.02 * 1e-10, direct_bond=True)")
+uf.desc[-1].add_prompt("relax> relax_data.dipole_pair(spin_id1='@N', 
spin_id2='@H', ave_dist=1.02 * 1e-10, direct_bond=True)")
 uf.backend = relax_data.dipole_pair
 uf.menu_text = "dipole_&pair"
 uf.wizard_height_desc = 350
 uf.wizard_size = (900, 700)
-uf.wizard_image = WIZARD_IMAGE_PATH + 'fid.png'
+uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 
'NH_dipole_pair.png'
 
 
 # The relax_data.display user function.