relax SVN archive

Replaced the table in the frame_order.permute_axes user function.

The original table was an old and incorrect version. This has been replaced by the correct
permutation table.

Updated the description of the frame_order.permute_axes user function.

This now includes the isotopic cone.

The pivot point can now be excluded from the grid search in the frame order auto-analysis.

If the initial pivot point is known to be reasonable, then it may be possible to skip it in the grid
search for the rotor frame order model. This can lead to a speed up of the analysis and can help
with stability. The pivot_search argument has been added to the auto-analysis
Optimisation.add_grid() method to enable this. The get_grid_pivot_search() method has also been
added to allow the auto-analysis to query this and turn it off if desired.

The minimise.execute user function skip_preset flag is now False in the frame order auto-analysis.

This is for the main model optimisation. Without this flag set, the grid search for the pivot point
position for the rotor model was being skipped at the first zoom level.

Redesigned the optimisation steps for the frame order auto-analysis.

The code has been significantly simplified as the optimisation for the PCS subset and full data set
was the same. The code duplication has been eliminated by combining it into the new optimisation()
method. The check for the PCS subset has also been expanded so that it is skipped if the subset
data pipe is not supplied, even if an optimisation object for the subset has been (this should
prevent strange errors when the auto-analysis is incorrectly used).

A side effect of this code merger is that the zooming grid search has now been activated for the
full PCS data set. This is of great benefit when a PCS subset is not being used.

Missing import.

The data pipe containing a PCS subset is now optional in the frame order auto-analysis.

This is for systems which have so little data that a subset makes no sense.

Merged revisions 26380-26383 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26380 | bugman | 2014-10-23 14:27:05 +0200 (Thu, 23 Oct 2014) | 6 lines

Created the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

This is to catch bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.
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r26381 | bugman | 2014-10-23 14:45:25 +0200 (Thu, 23 Oct 2014) | 13 lines

The structure.write_pdb user function can now handle empty molecules.

This fixes bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb user
function PDB files are incorrect after calling structure.delete.

To handle this consistently, the internal structural object ModelContainer.mol_loop() generator
method has been created. This loops over the molecules, yielding those that are not empty. The
MolContainer.is_empty() method has been fixed by not checking for the molecule name, as that remains
after the structure.delete user function call while all other information has been removed. And
finally the write_pdb() structural object method has been modified to use the mol_loop() method
rather than performing the loop itself.
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r26382 | bugman | 2014-10-23 14:55:09 +0200 (Thu, 23 Oct 2014) | 6 lines

Small modification of the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

File metadata is now being set to demonstrate that the structure.delete user function does not
remove this once there is no more data left for the molecule.
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r26383 | bugman | 2014-10-23 14:56:54 +0200 (Thu, 23 Oct 2014) | 8 lines

Fix for the structure.delete user function for molecule metadata once no more data exists.

This relates to bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.

The metadata, when it exists, is now deleted for the molecule once no more data is present.
........

Merged revisions 26380-26383 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26380 | bugman | 2014-10-23 14:27:05 +0200 (Thu, 23 Oct 2014) | 6 lines

Created the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

This is to catch bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.
........
r26381 | bugman | 2014-10-23 14:45:25 +0200 (Thu, 23 Oct 2014) | 13 lines

The structure.write_pdb user function can now handle empty molecules.

This fixes bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb user
function PDB files are incorrect after calling structure.delete.

To handle this consistently, the internal structural object ModelContainer.mol_loop() generator
method has been created. This loops over the molecules, yielding those that are not empty. The
MolContainer.is_empty() method has been fixed by not checking for the molecule name, as that remains
after the structure.delete user function call while all other information has been removed. And
finally the write_pdb() structural object method has been modified to use the mol_loop() method
rather than performing the loop itself.
........
r26382 | bugman | 2014-10-23 14:55:09 +0200 (Thu, 23 Oct 2014) | 6 lines

Small modification of the Structure.test_bug_22861_PDB_writing_chainID_fail system test.

File metadata is now being set to demonstrate that the structure.delete user function does not
remove this once there is no more data left for the molecule.
........
r26383 | bugman | 2014-10-23 14:56:54 +0200 (Thu, 23 Oct 2014) | 8 lines

Fix for the structure.delete user function for molecule metadata once no more data exists.

This relates to bug #22861 (https://gna.org/bugs/?22861), the chain IDs in the structure.write_pdb
user function PDB files are incorrect after calling structure.delete.

The metadata, when it exists, is now deleted for the molecule once no more data is present.
........

Merged revisions 26379 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26379 | bugman | 2014-10-23 14:17:31 +0200 (Thu, 23 Oct 2014) | 8 lines

The mol_name argument is now exposed in the structure.add_atom user function.

This has been added as the first argument of the user function to allow new molecules to be created
or to allow the atom to be placed into a specific molecule container. The functionality was already
implemented in the backend, so it has been exposed by simply adding a new argument definition to the
user function.
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