Author: bugman
Date: Sun Jul 15 16:12:00 2007
New Revision: 3341
URL: http://svn.gna.org/viewcvs/relax?rev=3341&view=rev
Log:
Application of Sebastien Morin's docstring and comments patch.
For the patch, see the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00038.html.
This patch (patch_consistency_tests__l1.2_r3340__docstrings_and_comments)
corrects docstrings and
comments errors which were remnants of the jw_mapping code from which the
consistency_tests code was
inspired. Also, this patch adds docstrings and comments to the code for
making it easier for users
to understand what the code actually does.
Modified:
branches/consistency_tests_1.2/maths_fns/consistency_tests.py
branches/consistency_tests_1.2/prompt/consistency_tests.py
branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
branches/consistency_tests_1.2/specific_fns/consistency_tests.py
branches/consistency_tests_1.2/test_suite/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=3341&r1=3340&r2=3341&view=diff
==============================================================================
--- branches/consistency_tests_1.2/maths_fns/consistency_tests.py (original)
+++ branches/consistency_tests_1.2/maths_fns/consistency_tests.py Sun Jul 15
16:12:00 2007
@@ -29,12 +29,23 @@
class Consistency:
def __init__(self, frq=None, gx=None, gh=None, mu0=None, h_bar=None):
- """Consistency tests for data acquired at different magnetic
fields."""
+ """Consistency tests for data acquired at different magnetic fields.
+
+ These three tests are used to assess the consistency of datasets
aquired at different
+ magnetic fields. Inconsistency can affect extracted information from
experimental data and
+ can be caused by variations in temperature, concentration, pH, water
suppression, etc.
+
+ 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
+ consistency functions proposed by Fushman D. et al. (1998) JACS,
120: 10947-10952.
+ """
# Initialise the data container.
self.data = Data()
- # Add the initial data to self.data
+ # Add the initial data to self.data.
self.data.gx = gx
self.data.gh = gh
self.data.mu0 = mu0
@@ -96,18 +107,27 @@
jwx = 1.0 / (3.0*d + c) * (r1 - 1.4*sigma_noe)
# 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.
p_2 = 0.5 * ((3.0 * (cos(orientation * pi / 180)) ** 2) -1)
# Calculate eta.
+ # eta is the cross-correlation rate between 15N CSA and 15N-1H
dipolar interaction. It is
+ # expressed here as proposed in Fushman D. & Cowburn D. (1998) JACS,
120: 7109-7110.
eta = ((d * c) ** 0.5) * (4.0 * j0 + 3.0 * jwx) * p_2
# Calculate F_eta.
+ # F_eta is independent of the magnetic field for residues with local
mobility
f_eta = eta * self.data.gh / (self.data.frq_list[0, 3] * (4.0 + 3.0
/ (1 + (self.data.frq_list[0, 1] * tc) ** 2)))
# Calculate P_HF.
+ # P_HF is the contribution to R2 from high frequency motions.
+ # P_HF = 0.5 * d * [J(wH-wN) + 6 * J(wH) + 6 * J(wH+wN)].
+ # Here, P_HF is described using a reduced spectral density approach.
p_hf = 1.3 * (self.data.gx / self.data.gh) * (1.0 - noe) * r1
# Calculate F_R2.
+ # F_R2 tests the consistency of the transverse relaxation data.
f_r2 = (r2 - p_hf) / ((4.0 + 3.0 / (1 + (self.data.frq_list[0, 1] *
tc) ** 2)) * (d + c/3.0))
# Return the three values.
Modified: branches/consistency_tests_1.2/prompt/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.2/prompt/consistency_tests.py?rev=3341&r1=3340&r2=3341&view=diff
==============================================================================
--- branches/consistency_tests_1.2/prompt/consistency_tests.py (original)
+++ branches/consistency_tests_1.2/prompt/consistency_tests.py Sun Jul 15
16:12:00 2007
@@ -1,7 +1,7 @@
###############################################################################
#
#
# Copyright (C) 2004-2005 Edward d'Auvergne
#
-# Copyright (C) 2007 Sebastien Morin <sebastien.morin.1 at ulaval.ca>
+# Copyright (C) 2007 Sebastien Morin <sebastien.morin.1 at ulaval.ca>
#
#
#
# This file is part of the program relax.
#
#
#
@@ -49,6 +49,7 @@
frq: The spectrometer frequency in Hz.
+
Description
~~~~~~~~~~~
Modified: branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.2/sample_scripts/consistency_tests.py?rev=3341&r1=3340&r2=3341&view=diff
==============================================================================
--- branches/consistency_tests_1.2/sample_scripts/consistency_tests.py
(original)
+++ branches/consistency_tests_1.2/sample_scripts/consistency_tests.py Sun
Jul 15 16:12:00 2007
@@ -25,7 +25,7 @@
# Set the approximate correlation time.
value.set(name, 13 * 1e-9, 'tc')
-# Select the frequency.
+# Set the frequency.
consistency_tests.set_frq(name, frq=600.0 * 1e6)
# Consistency tests.
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=3341&r1=3340&r2=3341&view=diff
==============================================================================
--- branches/consistency_tests_1.2/specific_fns/consistency_tests.py
(original)
+++ branches/consistency_tests_1.2/specific_fns/consistency_tests.py Sun Jul
15 16:12:00 2007
@@ -96,7 +96,7 @@
if frq_index == None:
continue
- # Set the r1, r2, and NOE to None.
+ # Set the R1, R2, and NOE to None.
r1 = None
r2 = None
noe = None
@@ -149,7 +149,7 @@
data.f_eta_sim = []
data.f_r2_sim = []
- # Reduced spectral density values.
+ # Consistency tests values.
data.j0_sim.append(j0)
data.f_eta_sim.append(f_eta)
data.f_r2_sim.append(f_r2)
@@ -189,11 +189,11 @@
tc: Correlation time.
- j0: Spectral density value at 0 MHz.
-
- f_eta: Eta test.
-
- f_r2: R2 test.
+ j0: Spectral density value at the zero frequency.
+
+ f_eta: Eta-test (from Fushman D. et al. (1998) JACS, 120:
10947-10952).
+
+ f_r2: R2-test (from Fushman D. et al. (1998) JACS, 120:
10947-10952).
"""
# Initialise.
@@ -215,8 +215,8 @@
def default_value(self, param):
"""
- Reduced spectral density mapping default values
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ Consistency testing default values
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
_______________________________________________________________________________________
| | |
|
@@ -287,7 +287,7 @@
def return_conversion_factor(self, stat_type):
- """Dummy function for returning 1.0."""
+ """Dummy function for returning 1.0. This function is essential when
writing grace files"""
return 1.0
Modified: branches/consistency_tests_1.2/test_suite/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.2/test_suite/consistency_tests.py?rev=3341&r1=3340&r2=3341&view=diff
==============================================================================
--- branches/consistency_tests_1.2/test_suite/consistency_tests.py (original)
+++ branches/consistency_tests_1.2/test_suite/consistency_tests.py Sun Jul 15
16:12:00 2007
@@ -39,7 +39,7 @@
# The test.
self.test = self.set_value
- # Spectral density calculation test.
+ # Consistency tests calculation test.
if test_name == 'calc':
# The name of the test.
@@ -58,7 +58,7 @@
# Setup.
self.calc_setup()
- # Try the reduced spectral density mapping.
+ # Try the consistency testing.
self.relax.interpreter._Minimisation.calc(self.run)
# Success.
@@ -66,6 +66,7 @@
def calc_integrity(self):
+ """The consistency tests calculation sub-routine."""
# Correct consistency functions values:
j0 = [4.0958793960056238e-09, 3.7976266046729745e-09]
@@ -103,6 +104,7 @@
def calc_setup(self):
"""Setup for the calculation test."""
+ # Locate and describe the data.
dir = sys.path[-1] + '/test_suite/data/jw_mapping/'
dataPaths = [dir + 'noe.dat',
@@ -136,7 +138,7 @@
# Set the approximate correlation time.
self.relax.interpreter._Value.set(self.run, 13 * 1e-9, 'tc')
- # Select the frequency.
+ # Set the frequency.
self.relax.interpreter._Consistency_tests.set_frq(self.run,
frq=600.0 * 1e6)
r3341 - in /branches/consistency_tests_1.2: maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/