Author: bugman
Date: Fri May 11 17:29:29 2012
New Revision: 16238
URL: http://svn.gna.org/viewcvs/relax?rev=16238&view=rev
Log:
Merged revisions 16222,16226-16229,16236 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r16222 | bugman | 2012-05-11 11:04:48 +0200 (Fri, 11 May 2012) | 6 lines
Merged the CHANGES file for relax version 1.3.16 back into the main 1.3
line.
The command used was:
svn merge -r16220:16221 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.16
........
r16226 | bugman | 2012-05-11 14:28:12 +0200 (Fri, 11 May 2012) | 12 lines
Ported the HTML user manual fix of r16225 from the 1.3.16 tag.
The command used was:
svn merge -r16224:r16225 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.3.16
.
.....
Removed more maths from the section titles of the HTML user manual.
This is an attempt at fixing the image brokenness of the HTML manual!
.....
........
r16227 | bugman | 2012-05-11 14:30:26 +0200 (Fri, 11 May 2012) | 6 lines
Fix for the creation of the HTML user manual
(http://www.nmr-relax.com/manual).
The shell command for renaming the relax_user_manual.html file to
index.html had a typo and was not
working!
........
r16228 | bugman | 2012-05-11 15:04:08 +0200 (Fri, 11 May 2012) | 7 lines
Fix for the HTML version of the relax user manual
(http://www.nmr-relax.com/manual/).
The model-free chapter subsection on the universal solution was causing
Latex2html to die! This is
the same as the fixes of r15816, but the \widehat maths command was
recently reintroduced into this
new section.
........
r16229 | bugman | 2012-05-11 15:06:24 +0200 (Fri, 11 May 2012) | 5 lines
A small edit of the "The universal solution" subsection title of the
model-free chapter.
This is for the relax HTML user manual
(http://www.nmr-relax.com/manual/Model_free_analysis.html).
........
r16236 | bugman | 2012-05-11 17:25:36 +0200 (Fri, 11 May 2012) | 3 lines
The scons 'clean' target now removes *.pyo files as well.
........
Modified:
branches/uf_redesign/ (props changed)
branches/uf_redesign/docs/CHANGES
branches/uf_redesign/docs/latex/model-free.tex
branches/uf_redesign/scons/manuals.py
branches/uf_redesign/sconstruct
Propchange: branches/uf_redesign/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri May 11 17:29:29 2012
@@ -1,1 +1,1 @@
-/1.3:1-16204
+/1.3:1-16237
Modified: branches/uf_redesign/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/docs/CHANGES?rev=16238&r1=16237&r2=16238&view=diff
==============================================================================
--- branches/uf_redesign/docs/CHANGES (original)
+++ branches/uf_redesign/docs/CHANGES Fri May 11 17:29:29 2012
@@ -1,3 +1,91 @@
+Version 1.3.16
+(11 May 2012, from /1.3)
+http://svn.gna.org/svn/relax/tags/1.3.16
+
+ Features:
+ * The scons 'install' target now creates both *.pyc and *.pyo files
during installation - this should result in faster relax startup times.
+ * The test suite now passes on the Fink relax installation on Mac OS
X as the ancient and very dead PyXML module is now being detected and worked
around.
+ * Renamed the 'pdc' user function class to 'bruker' and removed all
references to 'protein' - this is due to the Bruker absorption of the Protein
Dynamics Centre into the Bruker Dynamics Centre announced at
https://mail.gna.org/public/relax-users/2012-04/msg00011.html (Message-id:
<4F7AE13B.6010309@xxxxxxxxx>) by Dr. Klaus-Peter Neidig (peter dott neidig
att bruker-biospin dott de).
+ * Updates and improvements throughout the relax user manual.
+ * Added a new section to the introduction chapter of the user manual
for Gary Thompson's multi-processor framework.
+ * Added screenshots and descriptions of the graphical user interface
(GUI) to the introduction and all of the analysis chapters of the relax user
manual.
+ * The GUI and logging/teeing modes are now compatible with each
other.
+ * Expansion and completion of the model-free chapter of the relax
user manual.
+
+
+ Changes:
+ * Improved debugging of the observers in the status singleton object.
+ * Changed the behaviour of the arg_check module so that the
functions can return answers.
+ * The Bmrb.test_bmrb_rw GUI test now uses the base execute_uf()
method for the pipe.create call - this is part of the simplification of the
user function interfaces.
+ * A number of the pipe GUI user function front ends now use the
wizard page element_*() methods to simplify the code base.
+ * The wizard page element_string_list() method can now create the
special Combo_list objects.
+ * Created the wizard page ResetChoices() method for resetting the
list of values in a ComboBox.
+ * Created a Clear() wizard page method for clearing a specific GUI
element.
+ * The wizard page element_string() GUI element creator read_only
flag now defaults to False.
+ * The read_only=True flag to wizard_elements.Base_value now sets a
TextCtrl to the background colour.
+ * The wizard_elements.Base_value.SetValue() method now works
properly with the ComboBox.
+ * The wizard_elements.Base_value class now can set the element to be
read only.
+ * Created generic_fns.pipes.PIPE_DESC_LIST which is the PIPE_DESC as
a list, sorted by VALID_TYPES (to be used in the GUI user functions).
+ * Better ComboBox support in wizard_elements.Base_value class - now
strings and data are separate (if the data is supplied), and the GetValue()
method now returns the client data rather than the string value.
+ * Modified the wizard_elements.Base_value base GUI element class to
handle combo boxes.
+ * The Bmrb.test_bmrb_rw GUI test now uses the new execute_uf()
method for the bmrb.citation user function.
+ * Created the GUI test base method execute_uf() for executing a user
function.
+ * The bmrb.citation GUI user function now uses the new wizard page
element_*() methods for the GUI elements.
+ * Created a new wizard element for inputting integers.
+ * Created a new wizard element for inputting strings.
+ * Created the Bmrb.test_bmrb_rw GUI test.
+ * Completed the GUI interface for the bmrb.citation user function.
+ * Created a new wizard GUI element for lists of lists of strings.
+ * Abstracted out most of the String_list wizard element into the
List base class.
+ * The bmrb.citation GUI user function now uses the new wizard page
string list GUI element.
+ * Completed the wizard string list GUI element.
+ * Added the edit-rename Oxygen icons.
+ * Created a new String_list wizard GUI element class and associated
element_string_list() method.
+ * Created a new infrastructure in the wizards for handling more
advanced GUI elements.
+ * The Mf.test_write_results system test now checks for the ancient
PyXML.
+ * Added the xml module import tests to the dep_check module.
+ * The relax system information print out now includes information
about the XML modules.
+ * Added an initial but far from complete bmrb.citation user function
page and menu element.
+ * Added the BMRB icon in various sizes to the graphics directory and
icon paths.
+ * Updated all the BMRB user function front ends to the modern
docstring design.
+ * Created a special Bruker add icon for use in the relaxation data
GUI element.
+ * Added a button to the relaxation data GUI element for calling the
bruker.read user function.
+ * Improved the bruker.read user function docstring.
+ * Created the bruker.read GUI user function page and menu entry.
+ * Added the Bruker logo in various formats for use in the relax GUI.
+ * Converted the bruker.read user function prompt interface to the
new design.
+ * Renamed the PDC to Bruker DC in the test suite.
+ * Updated the development chapter of the relax user manual to be
more current - this includes removing the text saying that the GUI is yet to
be coded!
+ * Added mpi4py to the list of relax dependencies in the manual.
+ * Added GUI sections to the end of the NOE, R1+R2 and model-free
chapters of the user manual.
+ * The list of figures in the relax user manual is now on a new page.
+ * Updated the open source infrastructure chapter of the relax user
manual.
+ * Added a screenshot of the new relax 1.3.15 version in script mode.
+ * Significant updates to the introduction chapter of the relax user
manual: The text has been updated to match the current relax versions. All
mention of the dead SRLS theory has been eliminated. Screenshots of all the
GUI windows and analyses have been added to prettify the chapter, and the
text for the GUI has been rewritten for the new GUI design.
+ * Added a number of GUI screenshots for use in the relax user manual
- these were taken from http://www.nmr-relax.com/screenshots.html.
+ * Added colons to all entries of the abbreviation chapter in the
relax user manual.
+ * Updated and completed the installation chapter of the relax user
manual - a lot of the text was 4-6 years out of date.
+ * Some small edits to the release checklist document.
+ * Removed more maths from the HTML user manual section titles.
+
+
+ Bugfixes:
+ * Improved error reporting for multiple vectors in a model-free
analysis (bug #18807, https://gna.org/bugs/?18807).
+ * Updated the deselect.read user function call in the noe.py sample
script to match relax_fit.py (bug #19717, http://gna.org/bugs/?19717).
+ * The relax_fit.py sample script deselect.read user function now has
all columns specified (bug #19717, http://gna.org/bugs/?19717).
+ * Improved the error message system for the spin ID matching
multiple spins (bug #19717, http://gna.org/bugs/?19717).
+ * Fix for the test suite GUI tests - one of the state system tests
was removing the frame order analysis from the generic_fns.pipes.VALID_TYPES
list with a pop() call.
+ * Simplified the wizard_elements.Base_value ResetChoices() method -
this is an attempt to fix some racing conditions under wxGTK, triggered in
the test suite.
+ * Fix for the bmrb.citation user function documentation.
+ * The Mf.test_write_results system test now checks for the ancient
PyXML - this ancient version from 2004 which should be eliminated, if
installed, causes the toprettyxml() changes in Python 2.7.3 to be overridden.
+ * The alignment tensor user functions can now all handle the
situation whereby no tensors exist.
+ * Fix for the scons 'install' target for the byte-compilation of the
*.pyc files.
+ * Fix for the chi2 references in the maths chapter of the relax user
manual.
+ * Fix for the ANSI escape sequences for colouring text for when an
isatty() method does not exist.
+ * Fix for the creation of the HTML user manual
http://www.nmr-relax.com/manual/index.html file.
+
+
+
Version 1.3.15
(25 April 2012, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.15
Modified: branches/uf_redesign/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/docs/latex/model-free.tex?rev=16238&r1=16237&r2=16238&view=diff
==============================================================================
--- branches/uf_redesign/docs/latex/model-free.tex (original)
+++ branches/uf_redesign/docs/latex/model-free.tex Fri May 11 17:29:29 2012
@@ -1018,13 +1018,23 @@
% The local tm model-free models.
-\subsubsection{The local $\tau_m$ model-free models}
+\begin{latexonly}
+ \subsubsection{The local $\tau_m$ model-free models}
+\end{latexonly}
+\begin{htmlonly}
+ \subsubsection{The local $tau_m$ model-free models}
+\end{htmlonly}
Not only can the diffusion tensor be optimised as a global model affecting
all spins of the molecule but a set of model-free models can be constructed
in which each spin is assumed to diffuse independently. In these models a
single local $\tau_m$ parameter approximates the true, multiexponential
description of the Brownian rotational diffusion of the molecule. Each spin
of the macromolecule is treated independently. Another set of model-free
models which include the local $\tau_m$ parameter can be created and include
$tm0$ to $tm9$ (Models~\ref{model: tm0}--\ref{model: tm9} on page
\pageref{model: tm0}). These are simply models $m0$ to $m9$ with the local
$\tau_m$ parameter added. These models are an extension of the ideas
introduced in \citet{Barbato92} and \citet{Schurr94} whereby the model $tm2$,
the original Lipari and Szabo model-free equation with a local $\tau_m$
parameter, is optimised to avoid issues with inaccurate diffusion tensor
approximations.
% Determination of the diffusion tensor from the local tm parameter.
-\subsubsection{Determination of the diffusion tensor from the local $\tau_m$
parameter}
+\begin{latexonly}
+ \subsubsection{Determination of the diffusion tensor from the local
$\tau_m$ parameter}
+\end{latexonly}
+\begin{htmlonly}
+ \subsubsection{Determination of the diffusion tensor from the local
$tau_m$ parameter}
+\end{htmlonly}
In \citet{Bruschweiler95} and further investigated in \citet{Lee97}, a
methodology for determining the diffusion tensor from the local $\tau_m$
parameter together with the orientation of the XH bond represented by the
unit vector $\mu_i$ was presented. A local $\tau_m$ value was obtained for
each spin $i$ by optimising model $tm2$. The $\tau_{m,i}$ values were
approximated using the quadric model
\begin{equation} \label{eq: quadric}
@@ -1038,7 +1048,12 @@
% The universal solution.
%~~~~~~~~~~~~~~~~~~~~~~~~
-\subsection{The universal solution $\widehat\Univset$}
+\begin{latexonly}
+ \subsection{The universal solution $\Univset$}
+\end{latexonly}
+\begin{htmlonly}
+ \subsection{The universal solution $U$}
+\end{htmlonly}
The complex model-free problem, in which the motions of each spin are both
mathematically and statistically dependent on the diffusion tensor and vice
versa, was formulated using set theory in \citet{dAuvergneGooley07}. This
paper is important for understanding the entire concept of the new protocol
in relax and for truly grasping the complexity of the model-free problem.
The solution $\widehat\Univset$ to the model-free problem was derived as an
element of the universal set $\Univset$, the union of the diverse model-free
parameter spaces $\Space$. Each set $\Space$ was constructed from the union
of the model-free models $\Mfset$ for all spins and the diffusion parameter
set $\Diffset$. A single parameter loss on a single spin shifts optimisation
to a different space $\Space$. Ever since the seminal work of \citet{Kay89}
the model-free problem has been tackled by first finding an initial estimate
of the diffusion tensor and then determining the model-free dynamics of the
system (see Sections~\ref{sect: Mandel 1995} on page~\pageref{sect: Mandel
1995} and~\ref{sect: diffusion seeded paradigm} on page~\pageref{sect:
diffusion seeded paradigm}). This diffusion seeded paradigm is now highly
evolved and much theory has emerged to improve this path to the solution
$\widehat\Univset$. The technique can, at times, suffer from a number of
issues including the two minima problem of the spheroid diffusion tensor
parameter space, the appearance of artificial chemical exchange
\citep{Tjandra96}, the appearance of artificial nanosecond motions
\citep{Schurr94}, and the hiding of internal nanosecond motions caused by the
violation of the rigidity assumption \citep{Orekhov95b, Orekhov99b,
Orekhov99a}.
Modified: branches/uf_redesign/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/scons/manuals.py?rev=16238&r1=16237&r2=16238&view=diff
==============================================================================
--- branches/uf_redesign/scons/manuals.py (original)
+++ branches/uf_redesign/scons/manuals.py Fri May 11 17:29:29 2012
@@ -381,7 +381,7 @@
system(cmd)
# Create the proper index.html file.
- cmd = "cp -vp %s%srelax_user_manual.html %s%s index.html" % (dir,
path.sep, dir, path.sep)
+ cmd = "cp -vp %s%srelax_user_manual.html %s%sindex.html" % (dir,
path.sep, dir, path.sep)
print("Running the command:\n$ %s\n\n\n" % cmd)
system(cmd)
Modified: branches/uf_redesign/sconstruct
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/sconstruct?rev=16238&r1=16237&r2=16238&view=diff
==============================================================================
--- branches/uf_redesign/sconstruct (original)
+++ branches/uf_redesign/sconstruct Fri May 11 17:29:29 2012
@@ -407,7 +407,7 @@
print "###############################\n\n"
# Extensions of temporary files.
- temp_extns = ['pyc', 'bak', 'o', 'os', 'obj', 'exp', 'lib']
+ temp_extns = ['pyc', 'pyo', 'bak', 'o', 'os', 'obj', 'exp', 'lib']
# Print out.
print "\nRemoving the files ending in " + `temp_extns` + ".\n"
r16238 - in /branches/uf_redesign: ./ docs/CHANGES docs/latex/model-free.tex scons/manuals.py sconstruct