Author: bugman
Date: Tue Feb 17 09:47:30 2015
New Revision: 27659
URL: http://svn.gna.org/viewcvs/relax?rev=27659&view=rev
Log:
Merged revisions 27635-27639,27654-27655 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27635 | bugman | 2015-02-12 19:42:34 +0100 (Thu, 12 Feb 2015) | 10 lines
Created new system tests for implementing new functionality for the
structure.mean user function.
This includes the Structure.test_mean_models and
Structure.test_mean_molecules. The idea is to
convert the user function to the new pipes/models/molecules/atom_id design.
This will allow
molecules with non-identical sequences and atomic compositions to be
averaged. The set_mol_name and
set_model_num arguments from the structure.read_pdb,
structure.read_gaussian, and structure.read_xyz
user functions will also be implemented to allow the mean structure to be
stored alongside the other
molecules.
........
r27636 | bugman | 2015-02-13 17:05:57 +0100 (Fri, 13 Feb 2015) | 3 lines
Some fixes for the checks in the Structure.test_mean_molecules system test.
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r27637 | bugman | 2015-02-13 17:06:35 +0100 (Fri, 13 Feb 2015) | 3 lines
Fix for the structure.mean user function call in the
Structure.test_mean_models system test.
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r27638 | bugman | 2015-02-13 17:33:19 +0100 (Fri, 13 Feb 2015) | 7 lines
Expanded the checking in all the Structure.test_mean* system tests to cover
all atomic information.
This includes the Structure.test_mean, Structure.test_mean_models, and
Structure.test_mean_molecules
system tests. All structural data is now carefully checked to make sure
that the structure.mean
user function operates correctly.
........
r27639 | bugman | 2015-02-13 17:45:08 +0100 (Fri, 13 Feb 2015) | 15 lines
Converted the structure.mean user function to the new
pipe/model/molecule/atom_id design.
This allows the average structure calculation to work on atomic coordinates
from different data
pipes, different structural models, and different molecules. The user
function backend uses the new
pipe_control.structure.main.assemble_structural_coordinates() function to
assemble the common atom
coordinates, molecule names, residue names, residue numbers, atom names and
elements. All this
information is then used to construct a new molecule container for storing
the average structure in
the internal structural object.
To allow for the averaged structural data to be stored, the internal
structural object method
add_coordinates() has been created. This is modelled on the PDB, Gaussian,
and XYZ format loading
methods. The internal structural object mean() method is no longer used,
but remains for anyone who
might have interest in the future (though as it is untested, bit-rot will
be a problem).
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r27654 | bugman | 2015-02-17 09:27:42 +0100 (Tue, 17 Feb 2015) | 3 lines
Small correction for the structure.read_pdb user function description.
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r27655 | bugman | 2015-02-17 09:31:42 +0100 (Tue, 17 Feb 2015) | 6 lines
Created the Structure.test_read_merge_simultaneous system test.
This is to demonstrate a failure in the structure.read_pdb user function
when merging multiple
molecules from one file into one molecule simultaneously with a single user
function call.
........
Modified:
branches/nmrglue/ (props changed)
branches/nmrglue/lib/structure/internal/object.py
branches/nmrglue/pipe_control/structure/main.py
branches/nmrglue/test_suite/system_tests/structure.py
branches/nmrglue/user_functions/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/nmrglue/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/structure/internal/object.py?rev=27659&r1=27658&r2=27659&view=diff
Modified: branches/nmrglue/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/pipe_control/structure/main.py?rev=27659&r1=27658&r2=27659&view=diff
Modified: branches/nmrglue/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/structure.py?rev=27659&r1=27658&r2=27659&view=diff
Modified: branches/nmrglue/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/user_functions/structure.py?rev=27659&r1=27658&r2=27659&view=diff
r27659 - in /branches/nmrglue: ./ lib/structure/internal/ pipe_control/structure/ test_suite/system_tests/ user_functions/