Author: bugman
Date: Tue Oct 21 18:10:54 2014
New Revision: 26331
URL: http://svn.gna.org/viewcvs/relax?rev=26331&view=rev
Log:
Merged revisions 26307-26312,26321-26329 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26307 | bugman | 2014-10-17 16:13:04 +0200 (Fri, 17 Oct 2014) | 3 lines
Fix for the gui.fonts module to allow it to be used outside of the GUI.
........
r26308 | bugman | 2014-10-17 16:54:40 +0200 (Fri, 17 Oct 2014) | 5 lines
Updated all of the scripts in devel_scripts/gui/.
These have been non-functional since the merger of the bieri_gui back in
January 2011.
........
r26309 | bugman | 2014-10-17 16:55:44 +0200 (Fri, 17 Oct 2014) | 3 lines
The gui.misc.bitmap_setup() function can now be used outside of the GUI.
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r26310 | bugman | 2014-10-17 20:22:56 +0200 (Fri, 17 Oct 2014) | 3 lines
Fix for the GUI test base class new_analysis_wizard() method for relaxation
dispersion analyses.
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r26311 | bugman | 2014-10-18 10:20:36 +0200 (Sat, 18 Oct 2014) | 5 lines
Modified the pipe_control.pipes.get_bundle() function to operate when no
pipe is supplied.
In this case, the pipe bundle that the current data pipe belongs to will be
returned.
........
r26312 | bugman | 2014-10-18 10:22:07 +0200 (Sat, 18 Oct 2014) | 6 lines
Fix for the recently broken (r26306) Relax_disp.test_tp02_data_to_tp02
system test.
The data pipe bundle variable was no longer defined, so now it is retrieved
using the
pipe_control.pipes.get_bundle() function.
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r26321 | bugman | 2014-10-21 08:58:14 +0200 (Tue, 21 Oct 2014) | 3 lines
Bug fix for the structure.align user function for when no data pipes are
supplied.
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r26322 | bugman | 2014-10-21 13:52:10 +0200 (Tue, 21 Oct 2014) | 5 lines
Created the Periodic_table.has_element() method for the lib.periodic_table
module.
This is used to simply check if a given symbol exists as an atom in the
periodic table.
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r26323 | bugman | 2014-10-21 13:57:05 +0200 (Tue, 21 Oct 2014) | 3 lines
Added 4 unit tests to the _lib.test_periodic_table module for the
Periodic_table.has_element() method.
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r26324 | bugman | 2014-10-21 14:17:49 +0200 (Tue, 21 Oct 2014) | 8 lines
Modified the internal structural object backend for the structure.read_pdb
user function.
The MolContainer._det_pdb_element() method for handling PDB files with
missing element information
has been updated to use the Periodic_table.has_element() method to check if
the PDB atom name
corresponds to any atoms in the periodic table. This allows for far
greater support for HETATOMS
and all of the metals.
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r26325 | bugman | 2014-10-21 14:43:36 +0200 (Tue, 21 Oct 2014) | 7 lines
Created the Structure.test_load_spins_multi_mol system test.
This is to test yet to be implemented functionality of the
structure.load_spins user function. This
is the loading of spin information similar, but not necessarily identical
molecules all loaded into
the same structural model. For this, the from_mols argument will be added.
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r26326 | bugman | 2014-10-21 15:55:05 +0200 (Tue, 21 Oct 2014) | 6 lines
Fixes for the Structure.test_load_spins_multi_mol system test.
The call to the structure.load_spins user function has also been modified
so that all 3 spins are
loaded at the same time.
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r26327 | bugman | 2014-10-21 15:58:31 +0200 (Tue, 21 Oct 2014) | 8 lines
Implemented the multiple molecule merging functionality of the
structure.load_spins user function.
The argument has been added to the user function frontend and a description
added for this new
functionality. In the backend, the
pipe_control.structure.main.load_spins() function will now call
the load_spins_multi_mol() function if from_mols is supplied. This
alternative function is required
to handle missing atoms and differential atom numbering.
........
r26328 | bugman | 2014-10-21 17:03:49 +0200 (Tue, 21 Oct 2014) | 8 lines
Modified the N_state_model.test_populations system test to test the grid
search code paths.
This performs a grid search of one increment after minimisation, then
switches to the 'fixed'
N-state model and performs a second grid search of one increment. This now
tests currently untested
code paths in the grid_search() API method behind the minimise.grid_search
user function. The test
demonstrates a bug in the N-state model which was not uncovered in the test
suite.
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r26329 | bugman | 2014-10-21 17:56:08 +0200 (Tue, 21 Oct 2014) | 7 lines
Bug fix for the N-state model grid search when only alignment tensor
parameters are optimised.
The algorithm for splitting up the grid search to optimise each tensor
separately, hence massively
collapsing the dimensionality of the problem, was being performed
incorrectly. The grid_search()
API method inc, lower, and upper arguments are lists of lists, but were
only being treated as lists.
........
Removed:
branches/frame_order_cleanup/devel_scripts/gui/about_gui.py
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/devel_scripts/gui/about_model_free.py
branches/frame_order_cleanup/devel_scripts/gui/about_relax.py
branches/frame_order_cleanup/devel_scripts/gui/refs.py
branches/frame_order_cleanup/devel_scripts/gui/spin_create.py
branches/frame_order_cleanup/devel_scripts/gui/uf_sequence_read.py
branches/frame_order_cleanup/gui/fonts.py
branches/frame_order_cleanup/gui/misc.py
branches/frame_order_cleanup/lib/periodic_table.py
branches/frame_order_cleanup/lib/structure/internal/molecules.py
branches/frame_order_cleanup/pipe_control/pipes.py
branches/frame_order_cleanup/pipe_control/structure/main.py
branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
branches/frame_order_cleanup/test_suite/gui_tests/base_classes.py
branches/frame_order_cleanup/test_suite/gui_tests/relax_disp.py
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/populations.py
branches/frame_order_cleanup/test_suite/system_tests/structure.py
branches/frame_order_cleanup/test_suite/unit_tests/_lib/test_periodic_table.py
branches/frame_order_cleanup/user_functions/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Removed: branches/frame_order_cleanup/devel_scripts/gui/about_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/about_gui.py?rev=26330&view=auto
Modified: branches/frame_order_cleanup/devel_scripts/gui/about_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/about_model_free.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/devel_scripts/gui/about_relax.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/about_relax.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/devel_scripts/gui/refs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/refs.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/devel_scripts/gui/spin_create.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/spin_create.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/devel_scripts/gui/uf_sequence_read.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/devel_scripts/gui/uf_sequence_read.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/gui/fonts.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/fonts.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/gui/misc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/gui/misc.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/lib/periodic_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/periodic_table.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/lib/structure/internal/molecules.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/lib/structure/internal/molecules.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/pipe_control/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/pipes.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/pipe_control/structure/main.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/specific_analyses/n_state_model/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/n_state_model/api.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/test_suite/gui_tests/base_classes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/gui_tests/base_classes.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/test_suite/gui_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/gui_tests/relax_disp.py?rev=26331&r1=26330&r2=26331&view=diff
Modified:
branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/populations.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/scripts/n_state_model/populations.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/structure.py?rev=26331&r1=26330&r2=26331&view=diff
Modified:
branches/frame_order_cleanup/test_suite/unit_tests/_lib/test_periodic_table.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/unit_tests/_lib/test_periodic_table.py?rev=26331&r1=26330&r2=26331&view=diff
Modified: branches/frame_order_cleanup/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/structure.py?rev=26331&r1=26330&r2=26331&view=diff
r26331 - in /branches/frame_order_cleanup: ./ devel_scripts/gui/ gui/ lib/ lib/structure/internal/ pipe_control/ pipe_contro...