relax SVN archive

Ported r2599 from the 1.2 line.

The command used was:
$ svn merge -r2598:2599 svn+ssh://bugman@.../svn/relax/1.2

This changes 'Sconstruct' to 'SCons' in the relax manual.

Splitting of the 'pdb()' user function into 'pdb.read()' and 'pdb.vectors()' (task #3838).

These changes complete task #3838 (https://gna.org/task/?3838). The details of the changes were
discussed at https://mail.gna.org/public/relax-users/2006-10/msg00002.html (Message-id:
<7f080ed10610032153o4571935bq138d2739f55ca3bd@...>).

The only difference between the post proposing the changes and the actual changes is that the
proposed user function 'pdb.set_vectors()' is actually now called 'pdb.vectors()'.

Fix for bug #7297 (https://gna.org/bugs/index.php?7297).

This bug was reported by Alex Hansen. The problem was that relax was being too strict with the
checking of the Da and Dr diffusion tensor parameters. I have added a margin of error to these
checks to allow machine precision errors and optimisation precision issues (for the Method of
Multipliers constraint algorithm which allows the parameters outside of the limits).

Changed all references to Sconstruct in the manual to SCons. The program is really called SCons!

Completion of task #3630 (https://gna.org/task/?3630).

The unmodified Hessian and turning the line search off are no longer both specified by the string
'None'. Now they are specified by the regular expressions '^[Nn]o [Ll]ine [Ss]earch$' and
'^[Nn]o [Hh]essian [Mm]od' respecively.

This change implements half of task #3630 (https://gna.org/task/?3630).

The docstring in the generic optimisation function has been modified to clear up the ambiguity cased
by supplying the option 'None' together with Newton optimisation.

Ported the changes of r2595 of the 1.2 line into the 1.3 line.

The command used was:
$ svn merge -r2594:2595 svn+ssh://bugman@.../svn/relax/1.2

This changes the CSA value in the sample scripts to -172 ppm.

Changed the CSA value in the sample scripts from -170 ppm to -172 ppm.

This follows from discussions in the tread started by Sébastien Morin at
https://mail.gna.org/public/relax-users/2006-09/msg00042.html (Message-id:
<451C1910.6060108@...>).

Merged r2581 to r2593 of the 1.2 line into the 1.3 line.

The command used was:
svn merge -r2581:2593 svn+ssh://bugman@.../svn/relax/1.2

This merges a number of bug fixes: bug #7192 (https://gna.org/bugs/index.php?7192), bug #7224
(https://gna.org/bugs/?7224), bug #7225 (https://gna.org/bugs/index.php?7225), bug #7226
(https://gna.org/bugs/?7226), and bug #7241 (https://gna.org/bugs/?7241).

In addition, task #3781 (https://gna.org/task/?3781) has been completed, the sample script CSA values
have been changed from -160 ppm to -170 ppm, a regression test for catching bug #7224
(https://gna.org/bugs/?7224) has been added, and the Modelfree4 exit status is caught in all
situations.

Fix for bug #7241 (https://gna.org/bugs/?7241).

This is fix for the changes made at r2591 which were an attempt to fix the bug. Those changes did
not work though as the Scientific PDB data structure always contains the objects 'peptide_chains'
and 'nucleotide_chains'. Therefore these are now tested to see if they are empty rather than if
they exist.

The algorithm remains the same as in r2591, peptide chains are searched for and used first, then
nucleotide chains are searched for, and if neither are present RelaxNoPdbChainError is raised.