relax SVN archive

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.

Ported r2600 from the 1.2 line.

The command used was:
svn merge -r2599:2600 svn+ssh://bugman@.../svn/relax/1.2

This fixes bug #7297 (https://gna.org/bugs/index.php?7297).

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()'.