r6888 - /branches/rdc_analysis/maths_fns/rdc.py -- July 09, 2008 - 16:13

Author: bugman
Date: Wed Jul  9 16:13:45 2008
New Revision: 6888

URL: http://svn.gna.org/viewcvs/relax?rev=6888&view=rev
Log:
Created the average_rdc_5D() function.

This calculates the average RDC for an ensemble set of XH bond vectors, using 
the 5D alignment
tensor notation.


Modified:
    branches/rdc_analysis/maths_fns/rdc.py

Modified: branches/rdc_analysis/maths_fns/rdc.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/maths_fns/rdc.py?rev=6888&r1=6887&r2=6888&view=diff
==============================================================================
--- branches/rdc_analysis/maths_fns/rdc.py (original)
+++ branches/rdc_analysis/maths_fns/rdc.py Wed Jul  9 16:13:45 2008
@@ -19,6 +19,56 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA  
 #
 #                                                                            
 #
 
###############################################################################
-  
+
 # Module docstring.
 """Module containing functions for the calculation of RDCs."""
+
+
+def average_rdc_5D(vect, K, Axx, Ayy, Axy, Axz, Ayz):
+    """Calculate the average RDC for an ensemble set of XH bond vectors, 
using the 5D notation.
+
+    This function calculates the average RDC for a set of XH bond vectors 
from a structural
+    ensemble, using the 5D vector form of the alignment tensor.  The formula 
for this ensemble
+    average RDC value is::
+
+                    _K_
+                  1 \ 
+        <RDC_i> = -  >  RDC_ik (theta),
+                  K /__
+                    k=1
+
+    where K is the total number of structures,  k is the index over the 
multiple structures, RDC_ik
+    is the back-calculated RDC value for spin system i and structure k, and 
theta is the parameter
+    vector consisting of the alignment tensor parameters {Axx, Ayy, Axy, 
Axz, Ayz}.  The
+    back-calculated RDC is given by the formula::
+
+        RDC_ik(theta) = (x**2 - z**2)Axx + (y**2 - z**2)Ayy + 2x.y.Axy + 
2x.z.Axz + 2y.z.Ayz.
+
+
+    @param vect:        The XH bond vector matrix.  The first dimension 
corresponds to the
+                        structural index, the second dimension is the 
coordinates of the vector.
+    @type vect:         numpy matrix
+    @param K:           The total number of structures.
+    @type K:            int
+    @param Axx:         The xx component of the alignment tensor.
+    @type Axx:          float
+    @param Ayy:         The yy component of the alignment tensor.
+    @type Ayy:          float
+    @param Axy:         The xy component of the alignment tensor.
+    @type Axy:          float
+    @param Axz:         The xz component of the alignment tensor.
+    @type Axz:          float
+    @param Ayz:         The yz component of the alignment tensor.
+    @type Ayz:          float
+    """
+
+    # Initial back-calculated RDC value.
+    val = 0.0
+
+    # Loop over the structures k.
+    for k in xrange(K):
+        # Back-calculate the RDC.
+        val = val + (vect[k, 1]**2 - vect[k, 3]**2)*Axx + (vect[k, 2]**2 - 
vect[k, 3]**2)*Ayy + 2*vect[k, 1]*vect[k, 2]*Axy + 2*vect[k, 1]*vect[k, 
3]*Axz + 2*vect[k, 2]*vect[k, 3]*Ayz
+
+    # Return the average RDC.
+    return val / K