r2678 - /branches/tensor_pdb/generic_fns/pdb.py -- October 29, 2006 - 03:34

Author: bugman
Date: Sun Oct 29 03:34:21 2006
New Revision: 2678

URL: http://svn.gna.org/viewcvs/relax?rev=2678&view=rev
Log:
The unique axis of the spheroid is now represented by the Dpar unit vector in 
the tensor PDB.

As the Dpar unit vector has been added to the centre of mass to create a 
HETATM record, the distance
between the atom representing the centre of mass and the unique axis is 1 
Angstrom.


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=2678&r1=2677&r2=2678&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 03:34:21 2006
@@ -178,11 +178,33 @@
         hetatm.append(R)
 
 
+        # Axes of the tensor.
+        #####################
+
+        # Get 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
+
+            # Position relative to the center of mass.
+            pos = R + Dpar_unit
+
+            # Add the position as a HETATM.
+            hetatm.append(R + self.relax.data.diff[self.run].Dpar_unit)
+
+            # Print out.
+            print "    Unit vector:                 " + `Dpar_unit`
+            print "    Relative to center of mass:  " + `pos`
+
+
         # Connectivities.
         #################
 
-        #conect.append(['1', '2'])
-        #conect.append(['2', '1'])
+        conect.append(['1', '2'])
+        conect.append(['2', '1'])
 
 
         # Create the PDB file.