relax SVN archive

Fix for the package __all__ list checking unit tests - *.pyc files are now skipped.

Merged revisions 18732,18734-18752 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r18732 | bugman | 2013-03-09 13:28:52 +0100 (Sat, 09 Mar 2013) | 5 lines

Modified the release checklist document to use the stable release tags of minfx and bmrblib.

This is instead of the code in trunk which may not always be in a stable state.
........
r18734 | bugman | 2013-03-10 14:48:54 +0100 (Sun, 10 Mar 2013) | 9 lines

Redesign of the generic_fns.mol_res_spin.generate_spin_id() function.

The function now tries to generate a unique ID based on the spin information in the specified data
pipe. This is to attempt to fix a bug uncovered by the Structure.test_read_xyz_internal2 system
test. Defaulting in all cases to the spin name rather than spin number will often fail for a small
organic molecule, as the name in XYZ files is the atomic symbol and hence will almost never be
unique.
........
r18735 | bugman | 2013-03-10 14:50:01 +0100 (Sun, 10 Mar 2013) | 6 lines

Created the generic_fns.mol_res_spin.return_molecule_by_name() function.

This will be used in the future as it is much faster than generic_fns.mol_res_spin.return_molecule()
if the molecule name is already known.
........
r18736 | bugman | 2013-03-10 15:40:50 +0100 (Sun, 10 Mar 2013) | 9 lines

Bug fix for the maintenance of the spin ID lookup table metadata.

This is important for small molecules. Non-unique IDs were being placed into the lookup table,
resulting in incorrect spin containers being sometimes used. Now the molecule container has the
_res_name_count and _res_num_count metadata and the residue container the _spin_name_count and
_spin_num_count structures. These are updated via metadata_update() and are used by the
spin_id_variants() function to create a list of purely unique spin IDs.
........
r18737 | bugman | 2013-03-10 15:42:08 +0100 (Sun, 10 Mar 2013) | 3 lines

Missing import affecting the generic_fns.interatomic.create_interatom() function.
........
r18738 | bugman | 2013-03-10 15:44:44 +0100 (Sun, 10 Mar 2013) | 6 lines

Reverted the last revision (r18737) as it was not correct and RelaxErrors should be used instead.

The command used was:
svn merge -r18737:18736 .
........
r18739 | bugman | 2013-03-10 15:45:56 +0100 (Sun, 10 Mar 2013) | 5 lines

Fix for the generic_fns.interatomic.create_interatom() function.

RelaxNoSpinWarning has been replaced with RelaxNoSpinError.
........
r18740 | bugman | 2013-03-10 16:07:59 +0100 (Sun, 10 Mar 2013) | 3 lines

Fixes for the metadata update of the residue and spin name and number counts.
........
r18741 | bugman | 2013-03-10 16:11:03 +0100 (Sun, 10 Mar 2013) | 6 lines

Created the generic_fns.mol_res_spin.generate_spin_id_unique() function.

This will return a truly unique spin ID string based on the current molecule, residue, and spin data
structure.
........
r18742 | bugman | 2013-03-10 16:13:19 +0100 (Sun, 10 Mar 2013) | 6 lines

The spin_loop() function now uses generate_spin_id_unique() when the return_id flag is set.

This ensures that the caller received a unique spin ID which can be used to retrieve the
corresponding spin container.
........
r18743 | bugman | 2013-03-10 16:20:27 +0100 (Sun, 10 Mar 2013) | 5 lines

Fix for the new generate_spin_id_unique() function.

The precedence is now residue number then name, and spin name then number.
........
r18744 | bugman | 2013-03-10 16:25:07 +0100 (Sun, 10 Mar 2013) | 3 lines

Fix for the rdc.read user function for the recent spin ID metadata changes.
........
r18745 | bugman | 2013-03-10 17:01:34 +0100 (Sun, 10 Mar 2013) | 7 lines

Improved the generic_fns.mol_res_spin.generate_spin_id_unique() function.

This can now work with molecule, residue, and spin names and numbers alternatively to the containers
supplied as arguments. For this to work, the return_molecule_by_name() function has been improved
and the functions return_residue_by_info() and return_spin_by_info() have been added.
........
r18746 | bugman | 2013-03-10 21:28:56 +0100 (Sun, 10 Mar 2013) | 5 lines

The pcs.read user function backend now uses generic_fns.mol_res_spin.generate_spin_id_unique().

This allows the matching spin container to always be returned for storing the data.
........
r18747 | bugman | 2013-03-11 00:29:53 +0100 (Mon, 11 Mar 2013) | 5 lines

Large speed ups of the Bmrb system tests by the deletion of most of the residues.

On one system, this cuts the time for all 3 Bmrb tests from 70 to ~12 seconds.
........
r18748 | bugman | 2013-03-11 10:02:45 +0100 (Mon, 11 Mar 2013) | 5 lines

Added the profile flag keyword argument to the relax startup script for Unix-like systems.

This is to simplify the switching on of profiling.
........
r18749 | bugman | 2013-03-11 10:24:22 +0100 (Mon, 11 Mar 2013) | 6 lines

The spin_id argument to the residue.delete user function is no longer read-only.

This allows spin ranges or other complicated IDs to be specified. This is needed for the Bmrb GUI
tests to pass.
........
r18750 | bugman | 2013-03-11 10:47:48 +0100 (Mon, 11 Mar 2013) | 13 lines

Large cleanup and bugfixes for the molecule, residue, and spin data structure metadata maintenance.

The bugs fixed are important for non-protein molecules. For example is the spin name is not unique
per residue, or per molecule if no residues are defined, many parts of relax would fail.

All of the metadata_*() and spin_id_variants*() functions have been redesigned. It was also
identified that metadata_prune() was being used by different parts of relax for two different
purposes - the removal or pruning of metadata prior to the deletion of a data structure and the
clean up of no longer valid metadata. These two goals conflicted resulting in unpredictable
behaviour. Therefore the new metadata_cleanup() and spin_id_variants_cleanup() functions have been
created and the two behaviours separated.
........
r18751 | bugman | 2013-03-11 10:50:14 +0100 (Mon, 11 Mar 2013) | 8 lines

Fix for the bmrb.read user function for the recent molecule, residue and spin metadata improvements.

The generic_fns.bmrb.generate_sequence() function now calls generic_fns.mol_res_spin.metadata_clean()
to be sure that the metadata is correct. The problem is the structure of the BMRB file with no spin
information in the entity record, hence the residues are created first and the spins much later in
generate_sequence().
........
r18752 | bugman | 2013-03-11 11:13:42 +0100 (Mon, 11 Mar 2013) | 3 lines

Removed unused imports in the generic_fns.rdc module.
........

Removed unused imports in the generic_fns.rdc module.

Fix for the bmrb.read user function for the recent molecule, residue and spin metadata improvements.

The generic_fns.bmrb.generate_sequence() function now calls generic_fns.mol_res_spin.metadata_clean()
to be sure that the metadata is correct. The problem is the structure of the BMRB file with no spin
information in the entity record, hence the residues are created first and the spins much later in
generate_sequence().

Large cleanup and bugfixes for the molecule, residue, and spin data structure metadata maintenance.

The bugs fixed are important for non-protein molecules. For example is the spin name is not unique
per residue, or per molecule if no residues are defined, many parts of relax would fail.

All of the metadata_*() and spin_id_variants*() functions have been redesigned. It was also
identified that metadata_prune() was being used by different parts of relax for two different
purposes - the removal or pruning of metadata prior to the deletion of a data structure and the
clean up of no longer valid metadata. These two goals conflicted resulting in unpredictable
behaviour. Therefore the new metadata_cleanup() and spin_id_variants_cleanup() functions have been
created and the two behaviours separated.

The spin_id argument to the residue.delete user function is no longer read-only.

This allows spin ranges or other complicated IDs to be specified. This is needed for the Bmrb GUI
tests to pass.

Added the profile flag keyword argument to the relax startup script for Unix-like systems.

This is to simplify the switching on of profiling.

Large speed ups of the Bmrb system tests by the deletion of most of the residues.

On one system, this cuts the time for all 3 Bmrb tests from 70 to ~12 seconds.

The pcs.read user function backend now uses generic_fns.mol_res_spin.generate_spin_id_unique().

This allows the matching spin container to always be returned for storing the data.

Improved the generic_fns.mol_res_spin.generate_spin_id_unique() function.

This can now work with molecule, residue, and spin names and numbers alternatively to the containers
supplied as arguments. For this to work, the return_molecule_by_name() function has been improved
and the functions return_residue_by_info() and return_spin_by_info() have been added.