Author: bugman
Date: Thu May 1 15:01:47 2008
New Revision: 6026
URL: http://svn.gna.org/viewcvs/relax?rev=6026&view=rev
Log:
Updated the intro chapter to the new design.
Modified:
1.3/docs/latex/intro.tex
Modified: 1.3/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/intro.tex?rev=6026&r1=6025&r2=6026&view=diff
==============================================================================
--- 1.3/docs/latex/intro.tex (original)
+++ 1.3/docs/latex/intro.tex Thu May 1 15:01:47 2008
@@ -183,7 +183,7 @@
The arguments to a function are simply a comma separated list within the
brackets of the function. For example to save the program's current state
type
-\example{relax> state.save(`save', force=1)}
+\example{relax> state.save(`save', force=True)}
Two types of arguments exist in Python\index{Python|textbf} -- standard
arguments\index{argument} and keyword arguments\index{keyword
argument}\index{argument!keyword}. The majority of arguments you will
encounter within relax are keyword arguments however you may, in rare cases,
encounter a non-keyword argument. For these standard arguments just type the
values in, although they must be in the correct order. Keyword arguments
consist of two parts -- the key and the value. For example the key may be
\texttt{file} and the value you would like to supply is \texttt{`R1.out'}.
Various methods exist for supplying this argument. Firstly you could simply
type \texttt{`R1.out'} into the correct position in the argument list.
Secondly you can type \texttt{file=`R1.out'}. The power of this second
option is that argument order is unimportant. Therefore if you would like to
change the default value of the very last argument, you don't have to supply
values for all other arguments. The only catch is that standard arguments
must come before the keyword arguments.
@@ -203,7 +203,7 @@
Another special object is that of the function class\index{function class}.
This object is simply a container which holds a number of user functions.
You can access the user function within the class by typing the name of the
class, then a dot \texttt{`.'}, followed by the name of the user function.
An example is the user function for reading relaxation data out of a file and
loading the data into relax. The function is called \texttt{`read'} and the
class is called \texttt{`relax\_data'}. To execute the function, type
something like
-\example{relax> relax\_data.read(name, `R1', `600', 600.0 * 1e6,
`r1.600.out')}
+\example{relax> relax\_data.read(`R1', `600', 600.0 * 1e6, `r1.600.out')}
On first usage the relax prompt can be quite daunting. Two features exist
to increase the usability of the prompt -- the help system and tab completion.
@@ -252,7 +252,6 @@
model\_free.\_\_module\_\_ \\
model\_free.\_\_relax\_\_ \\
model\_free.\_\_relax\_help\_\_ \\
-model\_free.copy \\
model\_free.create\_model \\
model\_free.delete \\
model\_free.remove\_tm \\
@@ -264,32 +263,33 @@
-% The `run'.
-%~~~~~~~~~~~
-
-\subsection{The `run'}
-\index{run|textbf}
-
-Within relax the majority of operations are assigned to a special construct
called a `run'. For example to load relaxation data into the program it must
be committed to a pre-created `run'. Within one instance of relax multiple
runs can be created and various operations performed in sequence on these
runs. This is useful for operations such as model selection whereby the
function \texttt{`model\_selection'} can operate on a number of runs
corresponding to different models and then assign the results to a newly
created run.
-
-The flow of data through relax can be thought of as travelling through pipes
-- each pipe is synonymous with a run. User functions\index{user functions}
exist to transfer data between these pipes and other functions combine data
from multiple pipes into one or vice versa. The simplest invocation of relax
would be the creation of a single run and with the data being processed as it
is passing through this pipe.
-
-The primary method for creating a run is through the user
function\index{user functions} \texttt{`run.create'}. For example
-
-\example{relax> run.create(`m1', `mf')}
-
-will create a run called \texttt{`m1'}. The run is also associated with a
type which in this case is model-free analysis. The following is a table of
all the types which can be assigned to a run.
+% The data pipe.
+%~~~~~~~~~~~~~~~
+
+\subsection{The data pipe}
+\index{data pipe|textbf}
+
+Within relax all user functions operate on data stored within the current
data pipe. This pipe stores data is input, processed, or output as user
functions are called. There are different types of data pipe for different
analyses, e.g. a reduced spectral density mapping pipe, a model-free pipe, an
exponential curve-fitting pipe, etc. Multiple data pipes can be created
within relax and various operations performed in sequence on these pipes.
This is useful for operations such as model selection whereby the function
\texttt{`model\_selection'} can operate on a number of pipes corresponding to
different models and then assign the results to a newly created pipe. When
running relax you choose which pipe you are currently in by using the
\texttt{`pipe.switch'} user function to jump between pipes.
+
+The flow of data through relax can be thought of as travelling through these
pipes. User functions\index{user functions} exist to transfer data between
these pipes and other functions combine data from multiple pipes into one or
vice versa. The simplest invocation of relax would be the creation of a
single data pipe and with the data being processed as it is passing through
this pipe.
+
+The primary method for creating a data pipe is through the user
function\index{user functions} \texttt{`pipe.create'}. For example
+
+\example{relax> pipe.create(`m1', `mf')}
+
+will create a model-free data pipe labelled \texttt{`m1'}. The following is
a table of all the types which can be assigned to a data pipe.
\begin{center}
\begin{tabular}{ll}
\toprule
-Run type & Description \\
+Data pipe type & Description \\
\midrule
\texttt{`jw'} & Reduced spectral density mapping \\
\texttt{`mf'} & Model-free data analysis \\
+\texttt{`N-state'} & N-state model of domain motions \\
\texttt{`noe'} & Steady state NOE calculation \\
\texttt{`relax\_fit'} & Relaxation curve-fitting \\
\texttt{`srls'} & SRLS analysis \\
@@ -315,41 +315,43 @@
An example of a simple script which will minimise the model-free model `m4'
after loading six relaxation data sets is
\begin{exampleenv}
-\# Create the run. \\
+\# Create the data pipe. \\
name = `m4' \\
-run.create(name, `mf') \\
+pipe.create(name, `mf') \\
\\
\# Nuclei type \\
nuclei(`N') \\
\\
\# Load the sequence. \\
-sequence.read(name, `noe.500.out') \\
+sequence.read(`noe.500.out') \\
\\
\# Load the relaxation data. \\
-relax\_data.read(name, `R1', `600', 600.0 * 1e6, `r1.600.out') \\
-relax\_data.read(name, `R2', `600', 600.0 * 1e6, `r2.600.out') \\
-relax\_data.read(name, `NOE', `600', 600.0 * 1e6, `noe.600.out') \\
-relax\_data.read(name, `R1', `500', 500.0 * 1e6, `r1.500.out') \\
-relax\_data.read(name, `R2', `500', 500.0 * 1e6, `r2.500.out') \\
-relax\_data.read(name, `NOE', `500', 500.0 * 1e6, `noe.500.out') \\
+relax\_data.read(`R1', `600', 600.0 * 1e6, `r1.600.out') \\
+relax\_data.read(`R2', `600', 600.0 * 1e6, `r2.600.out') \\
+relax\_data.read(`NOE', `600', 600.0 * 1e6, `noe.600.out') \\
+relax\_data.read(`R1', `500', 500.0 * 1e6, `r1.500.out') \\
+relax\_data.read(`R2', `500', 500.0 * 1e6, `r2.500.out') \\
+relax\_data.read(`NOE', `500', 500.0 * 1e6, `noe.500.out') \\
\\
\# Setup other values. \\
-diffusion\_tensor.set(name, (2e-8, 1.3, 60, 290), param\_types=1,
axial\_type=`prolate', fixed=1) \\
-value.set(name, 1.02 * 1e-10, `bond\_length') \\
-value.set(name, -160 * 1e-6, `csa') \\
+diffusion\_tensor.init((2e-8, 1.3, 60, 290), param\_types=1,
axial\_type=`prolate', fixed=True) \\
+value.set(1.02 * 1e-10, `bond\_length') \\
+value.set(-160 * 1e-6, `csa') \\
+value.set(`15N', `heteronucleus') \\
+value.set(`1H', `proton') \\
\\
\# Select a preset model-free model. \\
-model\_free.select\_model(run=name, model=name) \\
+model\_free.select\_model(model=name) \\
\\
\# Grid search. \\
-grid\_search(name, inc=11) \\
+grid\_search(inc=11) \\
\\
\# Minimise. \\
-minimise(`newton', run=name) \\
+minimise(`newton') \\
\\
\# Finish. \\
-results.write(run=name, file=`results', force=1) \\
-state.save(`save', force=1)
+results.write(file=`results', force=True) \\
+state.save(`save', force=True)
\end{exampleenv}
Scripting is much more powerful than the prompt as advanced
Python\index{Python} programming can be employed (see the file
`full\_analysis.py' in the `sample\_scripts' directory for an example).
@@ -391,8 +393,22 @@
\subsection{Access to the internals of relax}
-To enable advanced Python\index{Python} scripting and control almost every
part of relax has been designed in an object oriented fashion. If you would
like to play with internals of the program the entirety of relax is
accessible within the object called \texttt{`self.relax'}. To access the raw
objects within relax which contain the program data the object called
\texttt{`self.relax.data'} stores all the data.
-
+To enable advanced Python\index{Python} scripting and control many parts of
relax have been designed in an object oriented fashion. If you would like to
play with internals of the program the entirety of relax is accessible by
importation. For example all data is contained within the object called the
relax data store which, to be able to access it, needs be imported by typing:
+
+\example{relax> from data import Data as relax\_data\_store}
+
+This is a dictionary type object which contains the multiple data pipes.
All of relax's packages, modules, functions, and classes are also accessible
by import statements. For example to create a rotation matrix from three
Euler angles in the z-y-z notation, type:
+
+\begin{exampleenv}
+relax> alpha = 0.1342 \\
+relax> beta = 1.0134 \\
+relax> gamma = 2.4747 \\
+relax> from maths\_fns.rotation\_matrix import R\_euler\_zyz \\
+relax> from numpy import float64, zeros \\
+relax> R = zeros((3,3), float64) \\
+relax> R\_euler\_zyz(R, alpha, beta, gamma) \\
+relax> R
+\end{exampleenv}
r6026 - /1.3/docs/latex/intro.tex