Author: bugman
Date: Tue Mar 28 08:51:05 2006
New Revision: 2426
URL: http://svn.gna.org/viewcvs/relax?rev=2426&view=rev
Log:
Merged r2424:2425 of the 'diff_tensor_bug_5559_fix' branch back into the main
development line.
The command used was:
svn merge -r2424:2425
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/diff_tensor_bug_5559_fix/ .
These changes fix bug #5559 at
https://gna.org/bugs/?func=detailitem&item_id=5559.
Modified:
1.2/data.py
1.2/test_suite/diffusion_tensor.py
Modified: 1.2/data.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/data.py?rev=2426&r1=2425&r2=2426&view=diff
==============================================================================
--- 1.2/data.py (original)
+++ 1.2/data.py Tue Mar 28 08:51:05 2006
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003, 2004 Edward d'Auvergne
#
+# Copyright (C) 2003, 2004, 2006 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -43,7 +43,7 @@
self.pdb = SpecificData()
# Diffusion data.
- self.diff = SpecificData()
+ self.diff = DiffTensorData()
# The residue specific data.
self.res = Residue()
@@ -134,6 +134,80 @@
+# Diffusion tensor specific data.
+#################################
+
+class DiffTensorData(SpecificData):
+ def __init__(self):
+ """Dictionary type class for the diffusion tensor data.
+
+ The non-default diffusion parameters are calculated on the fly.
+ """
+
+
+ def add_item(self, key):
+ """Function for adding an empty container to the dictionary.
+
+ This overwrites the function from the parent class SpecificData.
+ """
+
+ self[key] = DiffTensorElement()
+
+
+
+class DiffTensorElement(Element):
+ def __init__(self):
+ """An empty data container for the diffusion tensor elements."""
+
+
+ def __getattr__(self, name):
+ """Function for calculating the parameters on the fly."""
+
+ # All tensor types.
+ ###################
+
+ # Diso.
+ if name == 'Diso':
+ return 1.0 / (6.0 * self.tm)
+
+
+ # Spheroidal diffusion.
+ #######################
+
+ # Dper = Diso - 1/3Da.
+ if name == 'Dper':
+ return self.Diso - 1.0/3.0 * self.Da
+
+ # Dpar = Diso + 2/3Da.
+ if name == 'Dpar':
+ return self.Diso + 2.0/3.0 * self.Da
+
+ # Dratio = Dpar / Dper.
+ if name == 'Dratio':
+ return self.Dpar / self.Dper
+
+
+ # Ellipsoidal diffusion.
+ ########################
+
+ # Dx = Diso - 1/3Da(1 + 3Dr).
+ if name == 'Dx':
+ return self.Diso - 1.0/3.0 * self.Da * (1.0 + 3.0*self.Dr)
+
+ # Dy = Diso - 1/3Da(1 - 3Dr).
+ if name == 'Dy':
+ return self.Diso - 1.0/3.0 * self.Da * (1.0 - 3.0*self.Dr)
+
+ # Dz = Diso + 2/3Da.
+ if name == 'Dz':
+ return self.Diso + 2.0/3.0 * self.Da
+
+
+ # The attribute asked for does not exist.
+ raise AttributeError, name
+
+
+
# Residue specific data.
########################
Modified: 1.2/test_suite/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.2/test_suite/diffusion_tensor.py?rev=2426&r1=2425&r2=2426&view=diff
==============================================================================
--- 1.2/test_suite/diffusion_tensor.py (original)
+++ 1.2/test_suite/diffusion_tensor.py Tue Mar 28 08:51:05 2006
@@ -120,5 +120,5 @@
# Initialise some data.
self.relax.interpreter._Diffusion_tensor.init('sphere', 10e-9,
fixed=1)
- self.relax.interpreter._Diffusion_tensor.init('spheroid', (2e-8,
1.3, 60-360, 290), spheroid_type='prolate', fixed=1)
- self.relax.interpreter._Diffusion_tensor.init('ellipsoid', (9e-8,
0.5, 0.3, 60+360, 290, 100), fixed=0)
+ self.relax.interpreter._Diffusion_tensor.init('spheroid', (2e-8,
1.3, 60-360, 290), param_types=2, spheroid_type='prolate', fixed=1)
+ self.relax.interpreter._Diffusion_tensor.init('ellipsoid', (9e-8,
5e6, 0.3, 60+360, 290, 100), fixed=0)
r2426 - in /1.2: data.py test_suite/diffusion_tensor.py