Author: bugman
Date: Wed Feb 19 14:27:48 2014
New Revision: 22209
URL: http://svn.gna.org/viewcvs/relax?rev=22209&view=rev
Log:
Created two new LaTeX commands for improving the layout of Python code in the
relax manual.
These are \pysep and \pyus which will be used to format the Python module
separator character and
the Python underscore character respectively. They are used in the
\module{}, \pycode{}, etc.
commands to add the '.\linebreak[0]' and '\_\linebreak[0]' text to allow for
improved and consistent
line breaking.
Modified:
trunk/docs/latex/develop.tex
trunk/docs/latex/dispersion.tex
trunk/docs/latex/intro.tex
trunk/docs/latex/model-free.tex
trunk/docs/latex/relax.tex
Modified: trunk/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/develop.tex?rev=22209&r1=22208&r2=22209&view=diff
==============================================================================
--- trunk/docs/latex/develop.tex (original)
+++ trunk/docs/latex/develop.tex Wed Feb 19 14:27:48 2014
@@ -654,7 +654,7 @@
\item[Generic code:] This code includes classes and functions which are
independent of the UI and not specific to a certain data pipe type, for
example not being involved in model-free analysis, relaxation curve-fitting,
the NOE calculation, and reduced spectral density mapping. All this code is
located in the directory \directory{pipe\osus{}control\ossep{}}.
-\item[Specific setup:] This code implements the internal interface between
the generic and specific code. The generic code calls the specific setup
asking for a specific function for the given data pipe type. For example by
asking for the minimise function when the data pipe type is model-free
analysis the model-free specific \module{minimise()} method is returned.
Although the generic code accesses the specific code solely through this
interface the specific code can access the generic code directly. The code
is located in the file
\file{specific\osus{}fns\ossep{}specific\osus{}setup.py}.
+\item[Specific setup:] This code implements the internal interface between
the generic and specific code. The generic code calls the specific setup
asking for a specific function for the given data pipe type. For example by
asking for the minimise function when the data pipe type is model-free
analysis the model-free specific \pycode{minimise()} method is returned.
Although the generic code accesses the specific code solely through this
interface the specific code can access the generic code directly. The code
is located in the file
\file{specific\osus{}fns\ossep{}specific\osus{}setup.py}.
\item[Specific code:] This is the code which is specific to the data pipe
type -- model-free analysis, relaxation curve-fitting, reduced spectral
density mapping, and the NOE calculation. Each type is located in a separate
file in the directory \directory{specific\osus{}fns\ossep{}}.
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22209&r1=22208&r2=22209&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Wed Feb 19 14:27:48 2014
@@ -512,7 +512,7 @@
It is selected by setting the model to `NS CPMG 2-site expanded'.
The simple constraint $\pA > \pB$ is used to halve the optimisation space,
as both sides of the limit are mirror image spaces.
-This model will give the same results as the other numerical solutions
whereby $\RtwozeroA = \RtwozeroB$. The following is the set of equations of
the expansion used in relax. It has been modified from the original for
speed. See the \module{lib.dispersion.ns\_cpmg\_2site\_expanded} module for
more details including the original code. Further simplifications can be
found in the code.
+This model will give the same results as the other numerical solutions
whereby $\RtwozeroA = \RtwozeroB$. The following is the set of equations of
the expansion used in relax. It has been modified from the original for
speed. See the
\module{lib\pysep{}dispersion\pysep{}ns\pyus{}cpmg\pyus{}2site\pyus{}expanded}
module for more details including the original code. Further
simplifications can be found in the code.
\begin{subequations}
\renewcommand{\theequation}{\theparentequation .\arabic{equation}}
@@ -2421,7 +2421,7 @@
%~~~~~~~~~~~
\subsection{Dispersion script mode -- execution}
-Once the data has set up and you have modified your script to match your
analysis needs, then the data pipe, pipe bundle and analysis variables are
passed into the \module{Relax\linebreak[0]{}\_disp} class. This is the final
lines of the script:
+Once the data has set up and you have modified your script to match your
analysis needs, then the data pipe, pipe bundle and analysis variables are
passed into the \module{Relax\pyus{}disp} class. This is the final lines of
the script:
\begin{lstlisting}[firstnumber=129]
# Auto-analysis execution.
Modified: trunk/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/intro.tex?rev=22209&r1=22208&r2=22209&view=diff
==============================================================================
--- trunk/docs/latex/intro.tex (original)
+++ trunk/docs/latex/intro.tex Wed Feb 19 14:27:48 2014
@@ -127,7 +127,7 @@
\begin{description}
\item[The prompt] this is the primary interface of relax. Rather than
reinventing a new command language, relax's interface is the powerful Python
prompt. This gives the power user full access to a proven programming
language. See Figure~\ref{fig: relax prompt} for a screenshot.
\item[Scripting] this provides a more powerful and flexible framework for
controlling the program. The script will be executed as Python code enabling
advanced programming for automating data analysis. All the features available
within the prompt environment are accessible to the script. See
Figure~\ref{fig: relax script} for a screenshot.
-\item[GUI] the graphical user interface provides a sub-set of relax's
features - the automatic R$_1$ and R$_2$ relaxation rate curve-fitting, the
NOE calculations, and the automatic model-free analysis provided by the
\module{dauvergne\_protocol} module \citep{dAuvergneGooley08b}. See
Figure~\ref{fig: GUI screenshot - start} for a screenshot.
+\item[GUI] the graphical user interface provides a sub-set of relax's
features - the automatic R$_1$ and R$_2$ relaxation rate curve-fitting, the
NOE calculations, and the automatic model-free analysis provided by the
\module{dauvergne\pyus{}protocol} module \citep{dAuvergneGooley08b}. See
Figure~\ref{fig: GUI screenshot - start} for a screenshot.
\end{description}
@@ -531,7 +531,7 @@
\begin{description}
\item[Steady-state NOE:] this provides access to the steady-state NOE
calculation with pseudo Monte Carlo simulations for error analysis (this
falls back to bootstrapping as this is a calculation rather than
optimisation). See Figure~\ref{fig: screenshot: NOE analysis} on
page~\pageref{fig: screenshot: NOE analysis}.
\item[$\Rone$ and $\Rtwo$]: these provide easy access to optimisations and
error analysis for the $\Rone$ and $\Rtwo$ relaxation rates via exponential
curve-fitting (see Figures~\ref{fig: screenshot: R1 analysis} and~\ref{fig:
screenshot: R2 analysis} on pages~\pageref{fig: screenshot: R1 analysis}
and~\pageref{fig: screenshot: R2 analysis}).
-\item[Model-free analysis]: A fully automatic model-free protocol is
provided in another tab. This operates via the \module{dauvergne\_protocol}
module which implements the protocol of \cite{dAuvergneGooley08b} (see
Figure~\ref{fig: screenshot: model-free analysis} on page~\pageref{fig:
screenshot: model-free analysis}).
+\item[Model-free analysis]: A fully automatic model-free protocol is
provided in another tab. This operates via the
\module{dauvergne\pyus{}protocol} module which implements the protocol of
\cite{dAuvergneGooley08b} (see Figure~\ref{fig: screenshot: model-free
analysis} on page~\pageref{fig: screenshot: model-free analysis}).
\end{description}
A number of windows in the GUI provide user feedback or allow for the
viewing and editing of data. These include:
Modified: trunk/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/model-free.tex?rev=22209&r1=22208&r2=22209&view=diff
==============================================================================
--- trunk/docs/latex/model-free.tex (original)
+++ trunk/docs/latex/model-free.tex Wed Feb 19 14:27:48 2014
@@ -1312,7 +1312,7 @@
%~~~~~~~~~~~
\subsection{d'Auvergne protocol script mode -- execution}
-Once the data is set up and you have modified your script to match your
analysis needs, then the data pipe, pipe bundle and analysis variables are
passed into the \module{dAuvergne\linebreak[0]{}\_protocol} class. This is
the final line of the script:
+Once the data is set up and you have modified your script to match your
analysis needs, then the data pipe, pipe bundle and analysis variables are
passed into the \module{dAuvergne\pyus{}protocol} class. This is the final
line of the script:
\begin{lstlisting}[firstnumber=203]
# Execution.
Modified: trunk/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/relax.tex?rev=22209&r1=22208&r2=22209&view=diff
==============================================================================
--- trunk/docs/latex/relax.tex (original)
+++ trunk/docs/latex/relax.tex Wed Feb 19 14:27:48 2014
@@ -98,7 +98,9 @@
\newcommand{\ossep}{/\linebreak[0]}
\newcommand{\osus}{\_\linebreak[0]}
\newcommand{\pycode}[1]{{\small \texttt{#1}}}
+\newcommand{\pysep}{.\linebreak[0]}
\newcommand{\pystring}[1]{`{\small \texttt{#1}}'}
+\newcommand{\pyus}{\_\linebreak[0]}
\newcommand{\software}[1]{\texttt{#1}}
\newcommand{\no}{-}
\newcommand{\yes}{\checkmark}
r22209 - in /trunk/docs/latex: develop.tex dispersion.tex intro.tex model-free.tex relax.tex