Author: bugman
Date: Mon Mar 11 11:21:19 2013
New Revision: 18753
URL: http://svn.gna.org/viewcvs/relax?rev=18753&view=rev
Log:
Merged revisions 18732,18734-18752 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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.
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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.
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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.
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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 .
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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().
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r18752 | bugman | 2013-03-11 11:13:42 +0100 (Mon, 11 Mar 2013) | 3 lines
Removed unused imports in the generic_fns.rdc module.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/docs/Release_Checklist
branches/frame_order_testing/generic_fns/angles.py
branches/frame_order_testing/generic_fns/bmrb.py
branches/frame_order_testing/generic_fns/interatomic.py
branches/frame_order_testing/generic_fns/mol_res_spin.py
branches/frame_order_testing/generic_fns/pcs.py
branches/frame_order_testing/generic_fns/rdc.py
branches/frame_order_testing/generic_fns/structure/scientific.py
branches/frame_order_testing/relax
branches/frame_order_testing/specific_fns/model_free/results.py
branches/frame_order_testing/specific_fns/relax_fit.py
branches/frame_order_testing/test_suite/system_tests/scripts/bmrb_rw.py
branches/frame_order_testing/user_functions/residue.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/frame_order_testing/docs/Release_Checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/Release_Checklist?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/angles.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/bmrb.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/interatomic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/interatomic.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/mol_res_spin.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/pcs.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/rdc.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/scientific.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/relax?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/model_free/results.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/specific_fns/relax_fit.py?rev=18753&r1=18752&r2=18753&view=diff
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/bmrb_rw.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/bmrb_rw.py?rev=18753&r1=18752&r2=18753&view=diff
Modified: branches/frame_order_testing/user_functions/residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/user_functions/residue.py?rev=18753&r1=18752&r2=18753&view=diff
r18753 - in /branches/frame_order_testing: ./ docs/ generic_fns/ generic_fns/structure/ specific_fns/ specific_fns/model_fre...