r2688 - /branches/tensor_pdb/generic_fns/pdb.py -- October 29, 2006 - 04:08

Author: bugman
Date: Sun Oct 29 04:07:54 2006
New Revision: 2688

URL: http://svn.gna.org/viewcvs/relax?rev=2688&view=rev
Log:
Added the three axes corresponding to Dx, Dy, and Dz to the ellipsoid tensor 
PDB representation.

These are the eigenvalues of the ellipsoidal diffusion tensor.  Three carbon 
atoms were added to the
vector position and all were joined to the carbon representing the centre of 
mass (R).


Modified:
    branches/tensor_pdb/generic_fns/pdb.py

Modified: branches/tensor_pdb/generic_fns/pdb.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2688&r1=2687&r2=2688&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 04:07:54 2006
@@ -254,29 +254,54 @@
         # Axes of the tensor.
         #####################
 
-        # Get the unique axis of the spheroid.
+        # Create the unique axis of the spheroid.
         if self.relax.data.diff[self.run].type == 'spheroid':
             # Print out.
-            print "Calculating the Dpar unit vector (the unique axis of the 
diffusion tensor)."
-
-            # The Dpar unit vector.
-            Dpar_unit = self.relax.data.diff[self.run].Dpar_unit
+            print "Generating the unique axis of the diffusion tensor."
 
             # The Dpar vector.
-            Dpar_vect = Dpar_unit * self.relax.data.diff[self.run].Dpar * 
scale
+            Dpar_vect = self.relax.data.diff[self.run].Dpar_unit * 
self.relax.data.diff[self.run].Dpar * scale
 
             # Position relative to the center of mass.
-            pos = R + Dpar_vect
+            Dpar_vect = R + Dpar_vect
 
             # Add the atom and connect it to the center of mass.
-            self.atom_add(atom_id='Dpar', element='C', pos=pos)
+            self.atom_add(atom_id='Dpar', element='C', pos=Dpar_vect)
             self.atom_connect(atom_id='Dpar', bonded_id='R')
 
             # Print out.
-            print "    Scaling factor:              " + `scale`
-            print "    Unit vector:                 " + `Dpar_unit`
-            print "    Dpar vector (scaled):        " + `Dpar_vect`
-            print "    Relative to center of mass:  " + `pos`
+            print "    Scaling factor:                      " + `scale`
+            print "    Dpar vector (scaled + shifted to R): " + `Dpar_vect`
+            print
+
+        # Create the three axes of the ellipsoid.
+        if self.relax.data.diff[self.run].type == 'ellipsoid':
+            # Print out.
+            print "Generating the three axes of the ellipsoid."
+
+            # The Dx, Dy, and Dz vectors.
+            Dx_vect = self.relax.data.diff[self.run].Dx_unit * 
self.relax.data.diff[self.run].Dx * scale
+            Dy_vect = self.relax.data.diff[self.run].Dy_unit * 
self.relax.data.diff[self.run].Dy * scale
+            Dz_vect = self.relax.data.diff[self.run].Dz_unit * 
self.relax.data.diff[self.run].Dz * scale
+
+            # Positions relative to the center of mass.
+            Dx_vect = R + Dx_vect
+            Dy_vect = R + Dy_vect
+            Dz_vect = R + Dz_vect
+
+            # Add the atoms and connect them to the center of mass.
+            self.atom_add(atom_id='Dx', element='C', pos=Dx_vect)
+            self.atom_add(atom_id='Dy', element='C', pos=Dy_vect)
+            self.atom_add(atom_id='Dz', element='C', pos=Dz_vect)
+            self.atom_connect(atom_id='Dx', bonded_id='R')
+            self.atom_connect(atom_id='Dy', bonded_id='R')
+            self.atom_connect(atom_id='Dz', bonded_id='R')
+
+            # Print out.
+            print "    Scaling factor:                      " + `scale`
+            print "    Dx vector (scaled + shifted to R):   " + `Dx_vect`
+            print "    Dy vector (scaled + shifted to R):   " + `Dy_vect`
+            print "    Dz vector (scaled + shifted to R):   " + `Dz_vect`
             print