relax SVN archive

Created functions for calculating the center of mass of the selected residues.

The function 'self.center_of_mass()' in the file 'generic_fns/pdb.py' has been created to calculate
the center of mass. All unselected residues are skipped to allow hybrid models, two fused runs of
non-overlapping residues, to be handled. Hence the center of mass will be biased!

The function 'self.atomic_mass()' has also been added to the file. This function returns the atomic
mass corresponding to the supplied element string.

Created the user function 'pdb.create_tensor_pdb()'.

This is in response to the thread stating at
https://mail.gna.org/public/relax-devel/2006-10/msg00136.html (Message-id:
<7f080ed10610252045r3dcbba38q58aa53142af96e5a@...>).

This new user function creates a PDB file of artificial structures to represent the diffusion
tensor. The prompt interface function has been completed and the shell of the function
'self.create_tensor_pdb()' has been added to the file 'generic_fns/pdb.py'. This second function
solely tests that the run exists, that a PDB structure has been loaded, that the sequence has been
loaded, and then opens and then closes the PDB file. Hence an empty file is created by the user
function.

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