relax SVN archive

A branch for implementing the PDB representation of the Brownian rotational diffusion tensor.

Creating a PDB representation of the diffusion tensor was discussed at
https://mail.gna.org/public/relax-devel/2006-10/msg00136.html (Message-id:
<7f080ed10610252045r3dcbba38q58aa53142af96e5a@...>).

Roll-back of revision 2656 from 1.3 line:
svn merge -r 2657:2656 svn+ssh://macraild@.../svn/relax/1.3

see: https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

r2656 was accidentally applied to the 1.3 line (intended for the apply
branch). r2662 merged the changes into the apply branch

Merge of revision 2656 from 1.3 line.
svn merge -r 2655:2657 svn+ssh://macraild@.../svn/relax/1.3

This revision was accidentally applied to the 1.3 line.

Ported r2660 from the 1.2 line.

The command used was:
$ svn merge -r2659:2660 svn+ssh://bugman@.../svn/relax/1.2

This fixes an error when trying to plot the MC simulation data in reduced spectral density mapping
using the 'grace.write()' user function.

A fix for the error when trying to plot MC sim data with reduced spectral density mapping.

This problem was reported by Daniel Perez (daniel dot perez at mol dot biol dot ethz dot ch) in the
post at https://mail.gna.org/public/relax-users/2006-10/msg00043.html (Message-id:
<453C7154.4040603@...>).

In case this fix isn't for the same problem (no traceback was provided), the error message that this
solves is reproduced at https://mail.gna.org/public/relax-users/2006-10/msg00045.html (Message-id:
<7f080ed10610230104w3a873225hd5481581886efacf@...>).

The problem was the the function 'return_values' in the file 'specific_fns/jw_mapping.py' was
a copy of an ancient function which did not support MC simulation data. All other types of analysis
were using the function from their common base class. By deleting this ancient code, the base class
function is utilised and the grace.write() user function now works with simulation data.

Ported r2658 from the 1.2 line.

The command used was:
$ svn merge -r2657:2658 svn+ssh://bugman@.../svn/relax/1.2

These changes complete task #4002 (https://gna.org/task/index.php?4002), the implementation of the
'grace.write()' user function for reduced spectral density mapping.

Completion of task #4002 (https://gna.org/task/index.php?4002).

This task was created in response to Daniel Perez's (daniel dot perez at mol dot biol dot ethz dot
ch) post at https://mail.gna.org/public/relax-users/2006-10/msg00040.html (Message-id:
<4539BABA.80204@...>).

Three things were required:

1. The pre-existing function self.relax.specific.jw_mapping.return_conversion_factor was added to
the specific setup interface in 'specific_fns/specific_setup.py'.

2. The string 'J(0)' was not being recognised by the function
'self.relax.specific.jw_mapping.return_data_name' as the round brackets needed to be commented out
for the 'search' function to work.

3. The specific setup interface was returning the wrong 'return_grace_string' function. The
problem was that the model-free version of the function was being returned instead. The function
'return_units' was also that of model-free analysis instead of reduced spectral density mapping.

Removal of apply(func, args) calls from the minimisation code

As discussed at relax-devel:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

New branch of the 1.3 line for the removal of apply(func, args) calls

See the relax-devel discussion at:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

This fixes a bug in the compile re function.

The bug was reported by Alex Hansen at https://mail.gna.org/public/relax-devel/2006-10/msg00112.html
(Message-id: <481156b20610190725ud6bab67w1f8fbbdf849da52c@...>). The simple fix is
described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html (Message-id:
<7f080ed10610190738g7df6566fl13b74d9217071924@...>).