relax SVN archive

Fixed the nucleic acid residue names.

These names were being prefixed by 'R' by Scientific python, so residue 'G' would be labelled as
residue 'RG'! This was causing the user function 'pdb.vectors()' to fail as the residue was
expected to be called 'G'. The prefix 'R' is now stripped from the residue name.

Fixed a bug whereby the match re function had not been imported.

Creation of a rudimentary PDB file for representing the diffusion tensor.

The new function 'self.write_pdb_file()' has been added which creates a properly formatted PDB file.
It creates HET, HETNAM, and FORMUL records for the pseudo-residue 'TNS'. It also adds HETATM
records for each atom, adds the TER record, and then connects the appropriate atoms using CONECT
records. The file is terminated with the MASTER and END records. For a description of this, see
the post at https://mail.gna.org/public/relax-devel/2006-10/msg00136.html (Message-id:
<7f080ed10610252045r3dcbba38q58aa53142af96e5a@...>).

The function 'self.create_tensor_pdb()' has been modified to create the data for the new
'self.write_pdb_file()' function.

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.