Author: bugman
Date: Thu May 1 17:23:59 2008
New Revision: 6051
URL: http://svn.gna.org/viewcvs/relax?rev=6051&view=rev
Log:
Updated the development chapter to the new relax design.
Modified:
1.3/docs/latex/develop.tex
Modified: 1.3/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/develop.tex?rev=6051&r1=6050&r2=6051&view=diff
==============================================================================
--- 1.3/docs/latex/develop.tex (original)
+++ 1.3/docs/latex/develop.tex Thu May 1 17:23:59 2008
@@ -82,11 +82,8 @@
\begin{footnotesize}
\begin{verbatim}
- def delete(self, run):
+ def delete(self):
"""Function for deleting all model-free data."""
-
- # Arguments.
- self.run = run
\end{verbatim}
\end{footnotesize}
@@ -121,21 +118,45 @@
% Variables and functions.
\subsubsection{Variables and functions}
-For both variables and functions lower case with underscores between words
is always used. This is for readability as the convention is much more
fluent than camel case. A few rare exceptions exist, an example is the
Brownian diffusion tensor parameter of anisotropy $\Diff_a$ which is
referenced as \texttt{self.relax.data.diff[run].Da}. As a rule though all
new variable or function names should be kept as lower case. An example of
this convention for both the variable name and function name is:
+For both variables and functions lower case with underscores between words
is always used. This is for readability as the convention is much more
fluent than camel case. A few rare exceptions exist, an example is the
Brownian diffusion tensor parameter of anisotropy $\Diff_a$ which is
referenced as \texttt{cdp.diff\_tensor.Da}. As a rule though all new
variable or function names should be kept as lower case. An example of this
convention for both the variable name and function name is:
\begin{footnotesize}
\begin{verbatim}
- def assemble_param_names(self, index=None):
- """Function for assembling various pieces of data into a Numeric
array."""
+ def assemble_param_vector(self, spin=None, spin_id=None, sim_index=None,
model_type=None):
+ """Assemble the model-free parameter vector (as numpy array).
+
+ If the spin argument is supplied, then the spin_id argument will be
ignored.
+
+ @keyword spin: The spin data container.
+ @type spin: SpinContainer instance
+ @keyword spin_id: The spin identification string.
+ @type spin_id: str
+ @keyword sim_index: The optional MC simulation index.
+ @type sim_index: int
+ @keyword model_type: The optional parameter set, one of 'all',
'diff', 'mf', or
+ 'local_tm'.
+ @type model_type: str or None
+ @return: An array of the parameter values of the
model-free model.
+ @rtype: numpy array
+ """
# Initialise.
- self.param_names = []
+ param_vector = []
+
+ # Determine the model type.
+ if not model_type:
+ model_type = self.determine_param_set_type()
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
# Diffusion tensor parameters.
- if self.param_set == 'diff' or self.param_set == 'all':
- # Spherical diffusion.
- if self.relax.data.diff[self.run].type == 'sphere':
- self.param_names.append('tm')
+ if model_type == 'diff' or model_type == 'all':
+ # Normal parameters.
+ if sim_index == None:
+ # Spherical diffusion.
+ if cdp.diff_tensor.type == 'sphere':
+ param_vector.append(cdp.diff_tensor.tm)
\end{verbatim}
\end{footnotesize}
@@ -181,28 +202,35 @@
An example which shows most of these conventions is:
\begin{footnotesize}
\begin{verbatim*}
-from random import gauss
-
-
-class Monte_carlo:
- def __init__(self, relax):
- """Class containing functions for Monte Carlo simulations."""
-
- self.relax = relax
-
-
- def create_data(self, run=None, method=None):
- """Function for creating simulation data.
-
- It is assumed that all data types are residue specific.
+class Scientific_data(Base_struct_API):
+ """The Scientific Python specific data object."""
+
+ # Identification string.
+ id = 'scientific'
+
+
+ def __find_bonded_atom(self, attached_atom, mol_type, res):
+ """Find the atom named attached_atom directly bonded to the desired
atom.
+
+ @param attached_atom: The name of the attached atom to return.
+ @type attached_atom: str
+ @param mol_type: The type of the molecule. This can be one
of 'protein', 'nucleic acid',
+ or 'other'.
+ @type mol_type: str
+ @param res: The Scientific Python residue object.
+ @type res: Scientific Python residue instance
+ @return: A tuple of information about the bonded atom.
+ @rtype: tuple consisting of the atom number (int),
atom name (str), element
+ name (str), and atomic position (Numeric
array of len 3)
"""
- # Arguments.
- self.run = run
-
- # Test if the run exists.
- if not self.run in self.relax.data.run_names:
- raise RelaxNoPipeError, self.run
+ # Init.
+ bonded_found = False
+
+ # The attached atom is in the residue.
+ if attached_atom in res.atoms:
+ # The bonded atom object.
+ bonded = res[attached_atom]
\end{verbatim*}
\end{footnotesize}
@@ -612,11 +640,11 @@
\item[Other interfaces:] Any number of interfaces for example other GUIs,
an ncurses interface, a web based interface, or an MPI interface could be
added to relax without modification of the current sources.
-\item[Generic code:] This code includes classes and functions which are
independent of the UI and not specific to a certain run 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 \texttt{generic\_fns/}.
-
-\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 run type. For example by asking
for the minimise function when the run type is model-free analysis the
function \texttt{self.rel\-ax.spec\-if\-ic.mod\-el\_free.min\-im\-ise()} 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
\texttt{specific\_fns/specific\_setup.py}.
-
-\item[Specific code:] This is the code which is specific to the run 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 \texttt{specific\_fns/}.
+\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 \texttt{generic\_fns/}.
+
+\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 function
\texttt{self.rel\-ax.spec\-if\-ic.mod\-el\_free.min\-im\-ise()} 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 \texttt{specific\_fns/specific\_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 \texttt{specific\_fns/}.
\item[Mathematical functions:] This is reserved for CPU intensive code
involved in calculations. The code may be written in Python however C code
can be used to significantly increase the speed of the calculations. For
optimisation the code can include function evaluations, calculation of
gradients, and calculation of Hessians. These functions are located in the
directory \texttt{maths\_fns/}.
r6051 - /1.3/docs/latex/develop.tex