r16933 - /branches/interatomic/user_functions/dipole_pair.py -- June 18, 2012 - 14:41

Author: bugman
Date: Mon Jun 18 14:41:55 2012
New Revision: 16933

URL: http://svn.gna.org/viewcvs/relax?rev=16933&view=rev
Log:
Refinement of the dipole_pair user function definitions.


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=16933&r1=16932&r2=16933&view=diff
==============================================================================
--- branches/interatomic/user_functions/dipole_pair.py (original)
+++ branches/interatomic/user_functions/dipole_pair.py Mon Jun 18 14:41:55 
2012
@@ -39,12 +39,12 @@
 uf_class = uf_info.add_class('dipole_pair')
 uf_class.title = "Class for manipulating magnetic dipole-dipole 
interactions."
 uf_class.menu_text = "&dipole_pair"
-uf_class.gui_icon = "relax.fid"
+uf_class.gui_icon = "relax.dipole_pair"
 
 
 # The dipole_pair.define user function.
 uf = uf_info.add_uf('dipole_pair.define')
-uf.title = "Define the pairs of spins involved in magnetic dipole-dipole 
relaxation interactions."
+uf.title = "Define the pairs of spins involved in magnetic dipole-dipole 
interactions."
 uf.title_short = "Magnetic dipole-dipole interaction setup."
 uf.add_keyarg(
     name = "spin_id1",
@@ -52,7 +52,7 @@
     py_type = "str",
     arg_type = "spin ID",
     desc_short = "first spin ID string",
-    desc = "The spin identification string for the first spin of the dipolar 
relaxation pair."
+    desc = "The spin identification string for the first spin of the dipolar 
pair."
 )
 uf.add_keyarg(
     name = "spin_id2",
@@ -60,20 +60,19 @@
     py_type = "str",
     arg_type = "spin ID",
     desc_short = "second spin ID string",
-    desc = "The spin identification string for the second spin of the 
dipolar relaxation pair."
+    desc = "The spin identification string for the second spin of the 
dipolar pair."
 )
 uf.add_keyarg(
     name = "direct_bond",
     default = True,
     py_type = "bool",
     desc_short = "directly bonded atoms flag",
-    desc = "This is a flag which if True means that the two spins are 
directly bonded.  This flag is useful to simply the set up of the main 
heteronuclear relaxation mechanism."
+    desc = "This is a flag which if True means that the two spins are 
directly bonded.  This flag is useful to simply the set up of the main 
heteronuclear relaxation mechanism or one-bond residual dipolar couplings."
 )
 # Description.
 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 average distances must be explicitly 
defined.")
+uf.desc[-1].add_paragraph("To analyse relaxation or residual dipolar 
coupling (RDC) data, pairs of spins which are coupled via the magnetic 
dipole-dipole interaction need to be specified.  This must process the use of 
the other user functions in this class.")
+uf.desc[-1].add_paragraph("For analyses which use relaxation data, 
specifying the dipole-dipole interaction will indicate that there is a 
dipolar relaxation mechanism operating between the two spins.  For RDC 
dependent analyses, this indicates that a residual dipolar coupling is 
expected between the two spins.")
 # Prompt examples.
 uf.desc.append(Desc_container("Prompt examples"))
 uf.desc[-1].add_paragraph("To define the protein 15N heteronuclear 
relaxation mechanism, type on of the following:")
@@ -81,6 +80,7 @@
 uf.desc[-1].add_prompt("relax> dipole_pair.define(spin_id1='@N', 
spin_id2='@H', direct_bond=True)")
 uf.backend = dipole_pair.define
 uf.menu_text = "&define"
+uf.gui_icon = "oxygen.actions.list-add-relax-blue"
 uf.wizard_height_desc = 350
 uf.wizard_size = (900, 700)
 uf.wizard_image = WIZARD_IMAGE_PATH + 'dipole_pair' + sep + 
'NH_dipole_pair.png'
@@ -125,6 +125,7 @@
 uf.desc[-1].add_prompt("relax> dipole_pair.set_dist(spin_id1='@N', 
spin_id2='@H', ave_dist=1.02 * 1e-10)")
 uf.backend = dipole_pair.set_dist
 uf.menu_text = "&set_dist"
+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'