r16920 - /branches/interatomic/user_functions/relax_data.py -- June 17, 2012 - 11:46

Author: bugman
Date: Sun Jun 17 11:46:11 2012
New Revision: 16920

URL: http://svn.gna.org/viewcvs/relax?rev=16920&view=rev
Log:
Added the definition for the new relax_data.dipole_pair user function.


Modified:
    branches/interatomic/user_functions/relax_data.py

Modified: branches/interatomic/user_functions/relax_data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/relax_data.py?rev=16920&r1=16919&r2=16920&view=diff
==============================================================================
--- branches/interatomic/user_functions/relax_data.py (original)
+++ branches/interatomic/user_functions/relax_data.py Sun Jun 17 11:46:11 2012
@@ -30,6 +30,7 @@
 # relax module imports.
 from generic_fns import pipes, relax_data
 from graphics import WIZARD_IMAGE_PATH
+from physical_constants import NH_BOND_LENGTH
 from user_functions.data import Uf_info; uf_info = Uf_info()
 from user_functions.objects import Desc_container
 
@@ -156,6 +157,57 @@
 uf.menu_text = "&delete"
 uf.gui_icon = "oxygen.actions.list-remove"
 uf.wizard_size = (700, 400)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'fid.png'
+
+
+# The relax_data.dipole_pair user function.
+uf = uf_info.add_uf('relax_data.dipole_pair')
+uf.title = "Define the pairs of spins involved in magnetic dipole-dipole 
relaxation interactions."
+uf.title_short = "Magnetic dipole-dipole interaction setup."
+uf.add_keyarg(
+    name = "spin_id1",
+    default = "@N",
+    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."
+)
+uf.add_keyarg(
+    name = "spin_id2",
+    default = "@H",
+    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."
+)
+uf.add_keyarg(
+    name = "dist",
+    default = NH_BOND_LENGTH,
+    py_type = "float",
+    desc_short = "interatomic distance (meters)",
+    desc = "The r^-3 averaged distance between the two spins to be used in 
the magnetic dipole constant."
+)
+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."
+)
+# 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 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.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'