r3377 - in /branches/consistency_tests_1.2: maths_fns/consistency_tests.py specific_fns/consistency_tests.py -- October 26, 2007 - 19:33

Author: bugman
Date: Fri Oct 26 18:30:20 2007
New Revision: 3377

URL: http://svn.gna.org/viewcvs/relax?rev=3377&view=rev
Log:
Application of a patch that complements information given to users on 
consistency testing.

The patch 'patch_1.2-r3375_consistency_branch__docstring' by Sebastien Morin 
(sebastien dot morin
dot 1 at ulaval dot ca) adds some text in docstrings or comments of files
'maths_fns/consistency_tests.py' and 'specific_fns/consistency_tests.py' to 
help users understand
why and how use the consistency tests.


Modified:
    branches/consistency_tests_1.2/maths_fns/consistency_tests.py
    branches/consistency_tests_1.2/specific_fns/consistency_tests.py

Modified: branches/consistency_tests_1.2/maths_fns/consistency_tests.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.2/maths_fns/consistency_tests.py?rev=3377&r1=3376&r2=3377&view=diff
==============================================================================
--- branches/consistency_tests_1.2/maths_fns/consistency_tests.py (original)
+++ branches/consistency_tests_1.2/maths_fns/consistency_tests.py Fri Oct 26 
18:30:20 2007
@@ -37,9 +37,14 @@
 
         This code calculates three functions for each residue. When 
comparing datasets from
         different magnetic field, the value should be the same for each 
function as these are field
-        field independent. The J(0) function is the spectral density at the 
zero frequency and is
-        obtained using a reduced spectral density approach. The F_eta and 
F_R2 functions are the
+        independent. The J(0) function is the spectral density at the zero 
frequency and is obtained
+        using a reduced spectral density approach. The F_eta and F_R2 
functions are the
         consistency functions proposed by Fushman D. et al. (1998) JACS, 
120: 10947-10952.
+
+        To assess the consistency of its datasets, one should first 
calculate those values (J(0),
+        F_eta and F_R2) for each field. Then, the user should compare values 
obtained for different
+        magnetic fields. Comparisons could proceed using correlation plots 
and histograms, and the
+        user could also calculate correlation, skewness and kurtosis 
coefficients.
         """
 
         # Initialise the data container.
@@ -109,6 +114,9 @@
         # Calculate P_2.
         # p_2 is a second rank Legendre polynomial as p_2(x) = 0.5 * (3 * (x 
** 2) -1)
         # where x is the cosine of the angle Theta when expressed in radians.
+        #
+        # Note that the angle Theta (called 'orientation' in relax) is the 
angle between the 15N-1H
+        # vector and the principal axis of the 15N chemical shift tensor.
         p_2 = 0.5 * ((3.0 * (cos(orientation * pi / 180)) ** 2) -1)
 
         # Calculate eta.

Modified: branches/consistency_tests_1.2/specific_fns/consistency_tests.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.2/specific_fns/consistency_tests.py?rev=3377&r1=3376&r2=3377&view=diff
==============================================================================
--- branches/consistency_tests_1.2/specific_fns/consistency_tests.py 
(original)
+++ branches/consistency_tests_1.2/specific_fns/consistency_tests.py Fri Oct 
26 18:30:20 2007
@@ -417,8 +417,8 @@
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
         In consistency testing, only four values can be set, the bond 
length, CSA, angle
-        Theta and correlation time values.  These must be set prior to the 
calculation
-        of consistency functions.
+        Theta ('orientation') and correlation time values. These must be set 
prior to the
+        calculation of consistency functions.
 
         """