relax SVN archive

Ported r2611 from the 1.2 line.

The command used was:
$ svn merge -r2610:2611 svn+ssh://bugman@.../svn/relax/1.2

This adds the directory for Scons Python modules for the Builder functions.

Fixing the rest of bug #7241 (https://gna.org/bugs/?7241).

Bug #7241 was thought to be fixed in in r2591 and r2593, the commit messages describing the solution
being located at https://mail.gna.org/public/relax-commits/2006-09/msg00064.html (Message-id:
<E1GTgBi-0000R6-4h@...>) for r2591 and
https://mail.gna.org/public/relax-commits/2006-10/msg00001.html (Message-id:
<E1GTt6C-0005rk-8q@...>) for r2593.

However this was not the only place that the Scientific Python PDB data structure peptide_chains was
being accessed. The chains were being accessed in the file 'generic_fns/sequence.py' when the
sequence was being read out of the PDB file. This has now been modified with changes similar to
r2591 and r2593.

Created the directory 'scons' for splitting up the 'sconstruct' script into multiple Python modules.

Fix for bug #7336 (https://gna.org/bugs/index.php?7336).

The user function 'pdb.vectors()' was not set up properly. It was expecting the residue number to
be an integer and the residue name to be a string. However the default is that both are set to
None. This was causing a RelaxError.

Fix for bug #7335 (https://gna.org/bugs/index.php?7335).

The code which tests that the proton and heteronucleus have not been set to the same atom name has
been moved from the 'self.read()' function to the 'self.vectors()' function. Two more lines of
code, which were placing the atom names into the 'self.relax.data.pdb' data structure were also
identified to cause similar problems and were shifted from the read to the vectors function.

Fix for bug #7334 (https://gna.org/bugs/index.php?7334).

The problem was that the relax base class in the PDB class of 'prompt/pdb.py' was set to
'self.__relax__'. However two lines were attempting to use 'self.relax'.

Fix for bug #7333 (https://gna.org/bugs/index.php?7333).

The three tests of the test-suite have been modified to use the correct PDB functions. A few calls
to the user function 'pdb.vectors()' needed to be added and the 'heteronuc' and 'proton' argments
to the 'pdb.read()' funtion had to be removed.

Ported r2605 from the 1.2 line.

The command used was:
$ svn merge -r2604:2605 svn+ssh://bugman@.../svn/relax/1.2

This fixes bug #7277 (https://gna.org/bugs/?7277).

Fix for bug #7277 (https://gna.org/bugs/?7277).

This bug was reported by Alex Hansen. The problem was that the
'self.relax.generic_fns.palmer.create()' function was skipping spins when no relaxation data was
present whereas the complementary funtion 'self.relax.generic_fns.palmer.extract()' was not skipping
these spins. Hence the second of these functions was expecting more spins than were in the
modelfree4 generated 'mfout' file.

Created the JOBS file. This file describes the roles of the relax manager positions.