r16938 - /branches/interatomic/user_functions/dipole_pair.py -- June 18, 2012 - 17:59

Author: bugman
Date: Mon Jun 18 17:59:49 2012
New Revision: 16938

URL: http://svn.gna.org/viewcvs/relax?rev=16938&view=rev
Log:
Created the dipole_pair.unit_vectors user function definition.


Modified:
    branches/interatomic/user_functions/dipole_pair.py

Modified: branches/interatomic/user_functions/dipole_pair.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/dipole_pair.py?rev=16938&r1=16937&r2=16938&view=diff
==============================================================================
--- branches/interatomic/user_functions/dipole_pair.py (original)
+++ branches/interatomic/user_functions/dipole_pair.py Mon Jun 18 17:59:49 
2012
@@ -200,3 +200,31 @@
 uf.wizard_height_desc = 350
 uf.wizard_size = (900, 700)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 
'NH_dipole_pair.png'
+
+
+# The dipole_pair.unit_vectors user function.
+uf = uf_info.add_uf('dipole_pair.unit_vectors')
+uf.title = "Calculate the unit vectors between the magnetic dipole-dipole 
interactions."
+uf.title_short = "Magnetic dipole-dipole unit vector calculation."
+uf.add_keyarg(
+    name = "ave",
+    default = True,
+    py_type = "bool",
+    desc_short = "average vector flag",
+    desc = "A flag which if True will cause the bond vectors from all models 
to be averaged.  If vectors from only one model is extracted, this will have 
no effect."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("For an orientational dependent analysis, such as 
model-free analysis with the spheroidal and ellipsoidal global diffusion 
tensors or any analysis using RDCs, the unit vectors between the two dipoles 
must be calculated prior to starting the analysis.  For the unit vector 
extraction, the two interacting spins should already possess positional 
information, and the interaction defined via the dipole_pair.define user 
function.  This information will be used 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("The number of unit vectors per interaction will 
be defined by the number of positions each spin possesses together with the 
averaging flag.  If both spins have N positions loaded, the number of 
positions N for both must match.  In this case, as well as when one spin has 
N positions and the other a single position, then N unit vectors will be 
calculated.  This is unless the averaging flag is set, in which case an 
averaged unit vector of unit length will be calculated.")
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("To calculate the  the N-H distance for protein 
the 15N heteronuclear relaxation mechanism, type on of the following:")
+uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors('@N', '@H', 1.02 * 
1e-10)")
+uf.desc[-1].add_prompt("relax> dipole_pair.unit_vectors(spin_id1='@N', 
spin_id2='@H', ave_dist=1.02 * 1e-10)")
+uf.backend = dipole_pair.unit_vectors
+uf.menu_text = "&unit_vectors"
+uf.gui_icon = "oxygen.actions.edit-rename"
+uf.wizard_height_desc = 350
+uf.wizard_size = (900, 700)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 
'NH_dipole_pair.png'